I do prefer that they kept the recruit boosts from capturing sites, It encourages expansion and without that the only reason to expand would be for the recruiting citadel. The war forge and factory are useful for building an army quickly, but just one structure builds pretty fast. I find that (against A.I at least) I usually just capture the sites just to keep the enemy from getting the recruiting center within the area.
You do have a point, but one thing to note is that in the campaign mode, getting 10 free recruits per construction site made starting out with more Hunters than your opponent powerful - much more so if you didn't have any. It's probably better to not have one unit be quite so influential to the economy.
