When we examine the records of the treatments of Jews and other minorities under Islamic and secular governments in the Middle East, I don't think we can come to a conclusion that any secular government is superior to any Islamic government on the ethnic question.
It is the government of the secular Young Turks -- not the anti-Western Islamic Republic -- that stands accused of having committed massacres that some call a genocide against a minority, the Armenians. To this day, it's a taboo to speak of the massacres of Armenians as a genocide, as the recent experience of Orhan Pamuk, who was charged by the government with "insulting Turkishness" (which carries the potential sentence of up to three years) for his remarks on the subject, demonstrates (the charge was dropped four months later, thanks to the EU pressures).
Compare the conditions of Kurds under the Ba'athist government of Iraq, the Turkish government, the Ba'athist government of Syria, and the Iranian government. In Iraq, about 200,000 Kurds were displaced from the area that surrounds Kirkuk in 1975-78, and the Anfal campaign of 1986-89 (during the Iran-Iraq War and its aftermath) is estimated to have killed 100,000 Kurds. The Turkish government, in the course of counter-insurgency campaigns against the PKK, wiped off more than 3,000 Kurdish villages, killed more than 30,000 Kurds, and made more than 300,000 Kurds homeless. Leyla Zana, the first Kurdish woman MP in Turkey, spent ten years in prison for speaking Kurdish in the parliament, which brought charges of treason and so forth against her.
The Islamic Republic, too, has repressed Kurdish nationalism: about 10,000 Kurds were killed between 1979 and 1982 as the Revolutionary Guards fought the Democratic Party of Iranian Kurdistan and Komala. But the Iranian government has never denied the Kurds their language and culture, unlike the Turkish government, and Iran has been a host -- a "reluctant" one as it is -- to hundreds of thousands of Kurdish refugees fleeing from Iraq: "According to most accounts, at least 370,000 Iraqi Kurds have sought refuge in Iran since 1971, more than 100,000 of them in 1988. Given that the entire Kurdish population of Iraq is estimated at 3.5 million, this means that over 10 percent of all Iraqi Kurds are presently being housed by their eastern neighbor" ("Whatever Happened to The Iraqi Kurds?," 11 March 1991, <http://www.hrw.org/reports/1991/IRAQ913.htm#15>); and "With the end of the Persian Gulf War (1991), yet another Kurdish uprising against Iraqi rule was crushed by Iraqi forces; nearly 500,000 Kurds fled to the Iraq-Turkey border, and more than one million fled to Iran" ("Kurds," The Columbia Encyclopedia, Sixth Edition. 2001-05, <http://www.bartleby.com/65/ku/Kurds.html>). This may be changing if recent reports on the joint Iranian-Turkish campaign against the PKK are true, but it cannot be denied that the Kurds under the secular governments of Iraq and Turkey suffered more than the Kurds under the Islamic government of Iran. As for the Kurds of Syria, Amnesty International has this to say: "More than 200,000 Kurdish people in Syria are denied a nationality and passport. These stateless Kurds are denied some basic economic and social rights. They aren't allowed to own a house, land, or a business. They can't work as lawyers, journalists, engineers or doctors. Many are not allowed to study in school after the age of 14, and often they're not allowed treatment in state hospitals" ("Syria: A Culture Oppressed -- the Torture and Imprisonment of Syrian Kurds," <http://web.amnesty.org/pages/syr-100305-background-eng>). See, also, the AI overviews of Iran, Iraq, Syria, and Turkey today: <http://web.amnesty.org/report2006/irn-summary-eng> <http://web.amnesty.org/report2006/irq-summary-eng> <http://web.amnesty.org/report2006/syr-summary-eng> <http://web.amnesty.org/report2006/tur-summary-eng>. For members of minorities or anyone else for that matter, the most dangerous place to be is Iraq under the occupation led by the secular US government, what with US and coalition troops, Iraqi government forces, sectarian and ethnic militias, Iraqi guerrillas against the occupation, international terrorists, plain old criminals, and so on; and the secular governments of Syria and Turkey look no better than Iran.
As I said here before, the largest Jewish community in the Middle East outside Israel exists in Iran -- estimated to be about 25,000-35,000, down from 80,000 in 1979 (cf. <http://www.sephardicstudies.org/iran.html> and <http://arabworld.nitle.org/texts.php?module_id=6&reading_id=59&sequence=7>) -- whereas the other countries of the Middle East -- with the exception of Turkey, which has the second largest Jewish community in the Middle East, about 20,000, down from 90,000 in 1948 (cf. <http://arabworld.nitle.org/texts.php?module_id=6&reading_id=59&sequence=7>) -- have seen most of their Jewish communities flee from them.
The puppet government of Nuri as-Said ("fanatically pro-Western" in the words of Juan Cole and pro-Zionist) saw a majority of Iraq's Jewish community flee from the country (about 125,000 Iraqi Jews had fled to Israel by 1952, leaving only about 6,000) and froze their assets to boot.
After the independence of Algeria, a large majority (about 130,000) of its Jews left for France and a minority (about 26,000) left for Israel, and only about 100 are said to remain in Algeria today.
The 265,000-strong Jewish community of Morocco is now reduced to 5,500 or so.
About 30,000 Jews lived in Syria in 1948, but now only about 100 do.
Most of Yemen's 55,000 Jews left for Israel between 1949 and 1950 -- now only about 200 still live in that country.
The Jews of Lebanon, reputed to be the most secularized country of the Middle East, numbered around 20,000 in 1948, but now there remain only about 200, most Lebanese Jews having left their country in 1967.
About 38,000 Jews lived in Libya in 1948, but it looks like the Libyan Jews are down to the last one: "In 2002, the last known Jew in Libya, Esmeralda Meghnagi, died and it was thought that the long history of Jewry in Libya had ended[4];in 2002, however, it was discovered that Rina Debach, a then 80-year old woman, who was born and raised in Tripoli, but thought to be dead by her family in Rome, was still living in a nursing home in the country" (at <http://en.wikipedia.org/wiki/History_of_the_Jews_in_Libya>).
And how did Gamal Abdel-Nasser, an Arab nationalist perhaps most admired by secular leftists in the West, behave toward the Jews? His government expelled about 25,000 of them in 1956. By now, what used to be a 75,000-strong Jewish community in Egypt is said to have dwindled to fewer than 100.
[The estimated numbers cited above are from the Jewish Virtual Library and Wikipedia.]
Evidence just doesn't support the faith in automatic superiority of a secular government as far as the ethnic question is concerned (and that's evidence based solely on the Middle East, without including secular European nationalisms' records on the Jews and other minorities). What we can say with confidence is that the more ethnic and other unrests a country experiences, the more repressive its government becomes (e.g., in the case of Kurdish experience), and that discrimination intensifies when a minority is imagined to be associated with a hostile foreign power (e.g., in the case of Jewish experience). -- Yoshie <http://montages.blogspot.com/> <http://mrzine.org> <http://monthlyreview.org/>