I agree that the system says you don't kill someone unless you intend to. I think, however, there is something missing from that equation. When a character is going to do something, the GM gives feedback on the action, including mentioning his/her interpretation of the outcome of that action. In the most technical of interactions, this is the GM making sure he understands the outcome.
An example;
Harry is lining up to hit a goon who is pumping lead into the air out of a semi-automatic... with his car. He doesn't want to use a spell, and he's behind the wheel, so it just makes sense. Harry's player (that Jim guy?) tells the GM "Harry spins the wheel and bears down on the guy, ducking low to avoid the bullet as he runs him down." The GM nods, and thinks quick. "All right, the Blue Beetle will hit the goon and crush him, maybe killing him." If that isn't what "Jim" intends, he needs to clarify. He could say "I think he would be clipped, spun into the trash and knocked out," and that's fine. Because what Jim intends here is that Harry gets away from the goon, and that's the way he wants Harry's story to go. If he wanted Jim to do the same with magic, casting a Fuego spell at the goon, again, the GM might blink and say "So, he'll be a smoking pair of boots?". If Jim intends Harry to incinerate the goon, he'll say so. But it's not unfair, as a GM, to go to the players for clarification, and to remind the player that, to him or her, the action sounds homicidal.
The game isn't about trapping people into actions and outcomes. The story might be, but the player gets to let his or her character get lead into those events. Where this gets tricky is, indeed, with Compels. And then you have to look at your Aspects. If a player has chosen to take homicidal Aspects, is it wrong for the GM to use them? How is the character really the character is "I Eat Babies For Mana" doesn't get compelled when the lust for power rises? Why did the player make that character anyways if they complain when the Laws of that Universe set them up for the fall?
I don't see the game as a GM vs. Player interaction. I see it as a GM + Player collaboration. And part of that collaboration is that the GM needs to remind the player that reckless, homicidal abandon is... homicidal. Part of that is for the GM to compel those reckless, misanthropic Aspects the Player put on their sheet.
I support the original post. Killing with magic is killing with magic. Having made serious errors in life, they haunt you. Forever.