I'm not yet so sure Homura is overly powerful. But she's far more experienced and knowledgeable than any other magical girl we have seen so far for sure. In fact she might know than than whatever is behind Kyubey of some things. Pistols and hand grenades don't yet prove a whole lot in my opinion.

I suppose Madoka is a key to the grand plan of the witch faction and Homura's main concern is, indeed, to stop Madoka from becoming one. Though Kyebey could be right and there's no way Madoka can succeed in that. She might be better off allowing Madoka to become one and use the magnificent powers to alter the future instead of trying to stop it. Sayaka becoming a witch likely is a step toward the ruination that created the future Homura is attempting to prevent. All in all, though, Homura is too awkward to really affect Madoka or anybody through talk alone. Kind of like Tenshi from Angel Beats.