As far as I see it, we have three major options for what to do now:
1. Wander through the forest in the hopes of bumping into Mokou or a rabbit
There's a pretty significant chance we won't find anything, and moreover, the general direction we'd be headed in is vaguely back towards where we came, so there's a chance we may run into Marisa again. Of course, there's a chance we may run into her no matter where we go, but it seems the most likely with this option compared to others.
2. Head back to town and try speaking with Keine
Keine knows how to get to Mokou's (who in turn knows how to get to Eientei), and the current situation may be important enough for her to take time out to do so. Of course, she could also be in the middle of class. Additionally, we could pick up Tenshi while we're there, in case we need some extra firepower.
3. Head back up to the island we came here for originally
The celestials on the island may be able to tell us a bit more about what happened between Marisa and (probably) Eirin. Moreover, whoever she defeated ought to still be there, though there's a good chance they're not going to be in any shape to tell us anything for a little while. There is also, of course, the business we originally went there for. (This is a lower priority given things that have happened since then, but still)
While there's a chance of Marisa finding us no matter our action, I have a funny feel that Marisa is still groping around the forest, and hasn't given up and flown off, yet. Thus, I think our chances of being caught by her are best if we wander around, as opposed to simply leaving the forest and flying elsewhere. Worst comes to worst, if she is waiting for us above the canopy, we can just descend and run again and we won't be much worse off than we already are.
At this moment, I'm currently leaning towards 3, followed quickly thereafter by 2. Any other opinions?