Yes, but it likely will not preserve game balance. For example, a mere 4 extra CP per minifig could give them a whopping 4d10 armor and +1" movement. 2:1 odds would in no way be a fair fight against that, though CP costs would suggest so. It's fine for Heroes because they make for one big target, but on the army-scale it quickly gets ridiculous. Rediculous, even.
Of course this is easily rectified through a variety of houserules. If upgraded units have to spread the points evenly, Hero style, the CP gets diluted a bit (esp in movement), and if they can only upgrade so much before a mandatory step-up in size (with retroactive purchasing of existing capability), the CP cost to selectively pump one stat becomes exponential.
I actually prefer the second type of limiter, as that would let the minifigs use larger weapons more befitting to their super science. However, I'm sure I'm not the only one who's thought of an army of mini-heroes, so I figured I'd cast about for people's opinions and experiences before building my own.