They will eventually bring the MSQ to a solution that fits both parties. That is a GUARANTEE. They've already acknowledged the length is getting a bit much. I imagine it won't be too different than what they have in WoW, but I think the break points will be the story epochs themselves.

Starting points:
2.0 ARR -> 6.5
7.0 -> "Onward"

Depending on how 7.0 starts will likely determine if they will use it as a future starting point down the road or not, but I would imagine it's going to set us up on a different world / continent not Eorzea or the Source in order to transition narratively with no issue.
Your starting point then being, either the WoL who arrived here, or your character is from "new location". If you start your character there, you get a synopsis of events or you just get the lore book with information to read and generic entries to understand the characters motives and personailties.

Dungeons and Leveling would be probably be the main issue.

They could technically reset everyone to level 1 (probably the easiest thing to do), but allow those who crossed over to have all of their abilities out the gate (make people feel somewhat rewarded for the inconvenience of starting over), whereas those just starting a new character only have the skills as they level up. The only extension to this rule is that you are forced to choose a starting job, and the rest of your already leveled classes are either locked until you reach max level, or you can choose to start it over at level 1 if you want to play it immediately.

That's only an example of ways they can do it all and keep the balance attached to everyone, both new and old players. I'm sure they have other creative ways in planning already to approach it both narratively and balancing wise.