Hmm I don't clearly understand where WCAG actually breaks with bootstrap. It's just a responsive layout framework with a class composition approach and some basic functionality.
It should have nothing to do with it, i don't like it that much either but I found out that a big portion of the people just don't know enough to actually build a responsive homepage.
That's it about the technology. I think your reasoning is not conclusive but taste. Bootstrap and WCAG are not mutually exclusive. But stupid applications of any approach can lead to failed results.
To your concrete problem, I agree with Milica she puts it very reasonable.
You are the expert you were hired to give them advice, if they want to push another agenda, you either don't have enough evidence or they are ignorant.
I would rather push on the principles of how WCAG works and not against a specific technology, but if you really can't stand it -> her approach seams to be the most professional to me.