Thing is, if both go into the battle knowing what each other is capable of, both are going to try and use their powers as quick as possible. If Protege has no prep, he's going in there weak as could be to start off with and MM could erase Protege before he even has a chance to copy his powers.
Well, Molecule Man could get the jump on him with the first attack and wipe him from existence if he goes all out to start. But depending on where Protege is at and how many powers he's copied up until this point, he could have enough time/power to block MM's initial attack, copy his powers, and then effortlessly destroy him.
I'm going to say Protege, since Protege was pwning EVERYONE with ease. Frankly, I'm still not sure how Scathan was able to stop him.