Working with TWSTD being a justifiable choice actually just comes down to the means vs. ends debate, though. She had a multitude of choices with conflicting moral duties, and she chose some over others. It's up to you, whether she chose the right duties.

I suppose I'm a little confused by your argument. People argue that working with TWSITD was moral not because TWSITD were great dudes, but because it lead to a "greater good". It's fine to disagree with that, but the whole TWSITD situation was a great deal more complex than being able to drop them like a hot potato. You yourself acknowledge that it comes down to ends vs. means, and in the utilitarian mindset, the move is the only ethical one because it's the only one that leads to that desired greater good. The greater good being the disenfranchisement of the Church and the abolishment of feudalism.

From my perspective, she's saving a lot more lives this way. From yours, she crossed too many moral boundaries. Agree to disagree, eh?