Choices and consequences in Freedom Fighters mostly revolve around the order in which you complete missions if I recall. In one mission I think you could do a frontal assault on an important base, while they are unaware, but then they'd call in reinforcements and airsupport if you took too long.. You could've taken out the reinforcements and air support first, but that would've alert the base. So it's more like doing side mission to alleviate the main missions. I don't remember any ground breaking C&C build up at least.