To be fair, she’s not wrong in regards to the Theseus Ship problem. The concept in that is that Theseus’s ship constantly needs to get new parts, and eventually it is renovated so much that no parts of the original ship are there. So is it still Theseus’s ship?
And sure, you could wax poetic about it, but if Theseus still considers it his ship than it might as well be his ship.
That said, Misato the only way to solve the trolley problem is to beat up the guy who keeps tying people to the trolley tracks for an ethics-based quandary.