Not that this helps much because it's never really addressed in detail in the show, but based on what Nefcy said a couple years ago about Toffee being right but "going about things the wrong way" (which we now know refers to destroying magic), I think the difference is meant to be why they're doing it.
Ex. Toffee is clearly just destroying magic so there won't be a threat to his own power. He doesn't seem to be doing it for all monsterkind but just Septarians/his own followers specifically.
Star was doing it so monsters and Mewmans could have a chance to integrate without Mewmans lording their power over them. She and the Butterflys with her even specifically gave up the monarchy for the purpose of that even ground.
Also most significant difference: Toffee was obviously going to use the lack of magic to kill with no consequence, Star's not. If Toffee had succeeded in killing magic his kill count would've been higher just by what he was shown to have done already. Also why I hate to mention it since it was terrible, if Toffee had won Eclipsa and Globgor would never be freed, and in the show that's supposed to be bad because they were innocent and fought for monsters' rights. Star managed to destroy magic AND help free them AND get rid of a killer who likely would've continued his killing spree without any threats to his immortality.
I mean, the show's stupid, I'm really not even disagreeing with you fundamentally here (Eclipsa IS shit, they should have done/said more than just "Toffee was right" to get what I think was their intended message clearer), but Star was never killing for Toffee simply for destroying magic, but for having killed members of her family already and threatening Marco and her parents and kingdom. Stopping him for destroying magic in Battle for Mewni was more a byproduct of stopping his plans then entirely. It's not exactly equivalent.