IDK what the differences are if she rebuilds the seekers or not. My last playthrough I romanced her, and she said she would rebuild the seekers and it would take time. And that she was able to stay for now, that she will always stand by the inquisitors side. On the balcony she talks about how everyone is going to want to see the inquisitor, so she wants to enjoy the moment before he gets pulled away by all of the nobles, etc. who want to talk to him as Leliana alluded to.
Doing a playthrough right now where I told her to let the seekers go, so we'll see if there's any difference. The rebuild seeker ending is at least a variant of a happy ending, compared to the divine ending which pretty much suggests an end for the romance. I'm assuming if she doesn't seek to rebuild the seekers, she simply stays with the inquisition. Regardless she states "I will always stand by your side" so really you can't get more of a happier ending than that. I'll post here when I'm finished the "let the seekers go" version, I will let you know if there are any differences.