There are other magical means of killing. The Transmogrifian Torture, for example, is one. The reason that Avada Kedavra earns a life sentence in Azkaban is because it reliably (except in the case of Harry) kills its target, should it connect.
“Not nice,” he said calmly. “Not pleasant. And there’s no counter curse. There’s no blocking it.
Moody, The Unforgivable Curses, GoF
The Transmogrifian Torture is, I believe, similar to Crucio, in the way that is causes excruciating pain and slowly kills the victim. But this is different because there is a counter curse.
“It was definitely a curse that killed her — probably the Transmogrifian Torture — I’ve seen it used many times, so unlucky I wasn't there, I know the very counter curse that could have saved her
Lockhart, The Writing on the Wall, CoS
Had someone tortured another being using this spell, and another was to preform the counter curse, then the person who cast it would be charged with attempted murder, not actual, making it less reliable and not an Unforgivable Curse. It also probably a lot less brutal.
Sirius and Remus could have used a combination of two powerful damaging spells.
In the cases of Professor McGonagall getting hit with multiples running spells, and Snape by multiple Expelliarmus, both were harmed, and McGonagall was hospitalized when receiving a very strong stack of them, and Snape being knocked out cold for a few hours. It was possible that they were going to cast a spell that was very complex and powerful curse that would have stacked and killed Pettigrew.
The might have also wanted to share the blame.
If the Ministry figures out that Sirius and Lupin killed Pettigrew, even if they believe the story of Pettigrew being a Death Eater, the pair will still be punished if they used Avada Kedavra, or some other spell. They would want to share the blame, rather put all of the blame on one person's shoulders, say Sirius. They both might have also wanted revenge for Pettigrew killing James and Lily.