I'm really not okay with punishing people because someone else has strong feelings about it. If that's how we're doing things, why aren't we standing back while Anri kills the Pleiades Saints? Because she's not our friend and Sayaka is?Will it conflict with Anri's wish? If yes, it either won't hold, or it will some pretty terrible side effects on her.
Edit: About Oriko, remember that burning someone's house down is a real big deal. Like, sure we can shrug it off because we're just reading this, but imagine it from Sayaka's perspective. Her home is gone. All of her things. All the stuff she and her family kept there. Mementos, pictures, and just general stuff you collect over time.
Then there's the hardship it most definitely placed on her family. They're now indepted to someone else, their finances probably took a hit even if Hitomi's family shielded them from the worst of it.
Sure, saving the world is a great excuse for anything you want to do, but that doesn't mean it's one that the people you harm will accept. Or that they'll forgive you for what you did to do it. Especially not if Sayaka knew that they were likely planning to kill Madoka.
Some punishment is really needed. Seriously.
Punishment should be based on deterrent effect and public safety/recidivism risk. Nothing else.