I expect the former to force the latter.
I don't think Marco told her he was going after Star. When he comes home I expect that Jackie's going to be upset about him wasting the first few weeks of what was supposed to be their first summer together as a couple, enough that she'll finally confront him about how he keeps neglecting her for Star. They'll talk it out and Marco will resolve to finally make an effort to actively spend time with his girlfriend.
The new status quo of Marco going back and forth daily between Earth and Mewni will continue for a while, Marco will still hang out with Star a lot but they're not living together anymore. Star will be trying her best to be satisfied with just being friends with Marco, but of course her feelings are going to keep tempting her to push the boundaries of their friendship. Jackie ought to be wary of Star now, and I doubt Star's going to go out of her way to try to patch things up between them, but she's still a good person and trusts Marco so she'll tell herself that his visits to Mewni don't bother her so much, as long as he keeps making time for her like he promised.
Eventually though, Eclipsa will be freed, putting Star and Mewni itself in imminent danger. Marco will of course want to help his friend in her time of need again, but it's not the kind of situation that's going to be fixed in an afternoon, and it needs more attention than can be given just going back and forth every day.
Jackie's not okay with the idea of him leaving again, ditching her on Earth for a few more weeks of "their" summer. She's not going to ask him to choose, because she knows what he would do and his good reason for doing it, but it still hurts. She'll be the one to leave, sick of worrying about him, sick of being alone.
I like to think that the last thing she'll say to him is "I wish I had a friend like you."