I think both marxist and bourgeois political scientists have "the whole" in mind - it is that their concept of that whole differs considerably. For the bourgeois political scientists - the whole equals the sum of the component parts, which is evidenced, among others, by the Pareto optimum - if everyone reaches individual optimum, then the system is optimal. In other words, efficient operations of the component parts (individuals, firms) basically guarantees the efficiency of the whole.
Marxists, on th eother hand, believe not only that the whole is greater than the mere sum of the component parts, but that the whole is not a mere resultant of individual actions, but something that "causes" or "determines" those actions - a notion that is essentially alien to the neo-classical crowd.
However, I think that this diffrence has more to do with intellectual traditions - British versus Continental - than with politics. Bourgeois political economy was eveloped primarily by Brits, who tend to be philosophical nominalists (cf. David Hume) i.e. believing that only individual, directly observable phenomena exist, while their groupings is merely the work of human habit. The continental philsophical tradition tends toward philosophical realism - a belief that than not only directly observable individual phenomena, but also their groupins have real existence - a belief that underlies most of metaphysical thinking.
On the social level, philsophical realism can be manifested by institutionalism - a belief that society is not just a sum total of individual behaviors, but it consists of 'reified' behavioral patterns - or institutions - that determines individual actions. In that respect, marxists share turf with such reactionaries and nazi sympathizers as Talcott Parsons.
I think the difference lies in how those institutionalized patters are approached by researchers. Conservatives, that is, institutional determinists - view culture and other social-economic-political institutions as the "prime mover itself immovable" - i.e. something that causes all social action without itself being caused (it's easy to recognize parallels to the metaphysical concept of god in euroepan philosophy here). That is, social institutions either canno tbe changed, or changing them will be less than desirable (chaos). Radicals, otoh, take a more critical approach - while they belive that institutions "move" social action, they are not "immovable" - but can be changed, if critically examined, and such a change is often desirable.
This, btw, is why we should criticize "cultural determinism" i.e. the view asserting the primacy of culture in determining social action (e.g. identity and identity-related behaviour) - it is closer to the reactionary perspective of Talcott Parsons than to the critical perspective of Marx, Weber, Horkheimer or recently Touraine or Bourdieu.