Maybe you'll meet a girl who isn't interested in a long term relationship.
Should isn't actually be won't be? Are both acceptable?
I think both are acceptable. They are certainly correct.
It may help to consider that we often use the present when talking about future moments in English.
"When you arrive, we'll eat."
I think the main difference in your example is that "won't be" would imply that she starts to not want a long term relationship from when she meets you, versus the much more "in general", "she isn't interested", with you or with anyone.