Yes, I think this will happen and likely it will happen on a much shorter time-scale than a Scottish vote for independence and entry into the EU.
If there's another Scottish independence referendum, Scotland would gain independence from a NON-EU country (UK) and then apply to join. This is similar to the situation with Slovenia, which gained independence from Yugoslavia and then joined the EU. Spain didn't veto that.
Very slim chance though, seeing as it was mostly the Labour heartland that voted for Leave.