If they killed Peter Pettigrew, they could simply claim that he died in the course of his capture.  They don't need him to be alive to prove that Sirius was innocent; they just need his body.

Pettigrew was a Death Eater, who had successfully pinned one of his previous crimes on someone else, and who had managed to evade detection and capture for over a decade.  He's clearly a dangerous and ruthless individual who is capable of taking extreme acts to remain free (like pretending to be a pet rat for years at a time).  No one would blink an eye if you failed to bring him in alive.

Of course, telling that lie would require Lupin and Black to be less than perfectly honorable and scrupulous, but they weren't saints.