I'm not quite sure what this debate is about. There is nothing inherently impossible with having, for example a free market, representative governement, and slavery, for instance, socialist economics, democratic polity, and an aristocracy, or (hypothetically) green economics, a police state, and emancipation, or a free market-police state, etc. *** Whether or not these would all be workable in terms of game play is a different matter, but that's where the fun in playing comes in, yes?
As I recall, SMAC excluded certain social engineering choices from certain factions not because they were inconsistent with each other, but because they would have been inconsistent with the ideological choices of that particular faction (i.e., you couldn't go socialist if you played Morgan, the free-trader guy.)