Honestly, I've always liked that Mathilde has never really had to take part in political assassination and fuckery. Whenever she kills someone, it's because they're aligned with some dark force or faction, and pretty justified by their crimes. She's Grey, yes, but not dark grey, you know?
That said, she's also the kind of person who kills so others don't have to. Who walks into the darkest, bloodiest halls with a sword in her hand and a spell on her lips because maybe, just maybe, every drop of blood spilled by her hand is spared for another. Because somebody has to, somebody will, and it might as well be her. And, from what I've seen, she likes Boris. He fits pretty well into her demographic of favored rulers, even if she hasn't interacted with him too much.
So yeah, I think I could accept her doing this. The Tzar is an innocent man, as far as we know. Perhaps even a good man, in some respects. But Mathilde accepted long ago that it was her duty to be the blade in the dark, and I won't begrudge her fulfilling it this once.
Also more Mathilde mythology is always fun, even if this one is less pleasant than most.