I definitely think they are hinting at dark things to come for La'an, but then I also remember how she was when Pike saw her again in Quality of Mercy, even though that was a future event that could only happen if he were to avert his own fate. But, unless she was also somehow involved in what happens to him directly, I'm not sure how him avoiding his fate would have affected her so positively. I think at the time the writers were using her as a shorthand to show a time jump. And also hint at Una's upcoming trial. Except they had to know it would go well for her so bringing it up seems odd, in retrospect.
And right after that episode we saw La'an start to find ways to actually enjoy herself. She started dancing, making friends, etc. So at that time they must have had an arc in mind for her, and I feel it might still be true, and whatever is going on with her will end up being something that sucks but she is able to get past. Star Trek loves personal growth stories.
I suspect there actually was something on that ship in Ep2 and La'an is in their sights now and she's going to be forced to confront them again only the next time she, like Spock was able to, embraces all of who she is, (a carrier of augmented DNA, maybe still has some Vuclan left as well, still carrying so much survivors guilt, ect.) to get through it and comes out the other side lighter.
And I do hope they also tie wherever Una ends up back to the comment in Quality of Mercy. But it's because Una takes a commission where she is unavailable to her former crewmates, not that she got booted- which was what I think they were hinting at to make her trail later more dramatic.