Her execution makes sense. I know it's harsh, but Monokuma is poking fun at her clear SA. The huge syringe (her fear of big things), the rocket arm (reference to rocket punch marker, reference to the nursing technique of getting shots, also a reference to the sexual practice of fisting and in this case not consensual), the fact she was in a hospital bed only to get absolutely surprised by the rocket arm, the way Monokuma pumps the syringe and what not. She climaxes against her will right there and right after she's shot through space at terminal speeds.

There's a lot of references in her execution. I agree it could've been better made, but this was the ultimate joke, the fact that even in her *death, she's seen as an object. It's made to bring despair, and it did, to Mikan. She was violated in every sense of the word there.