It's not like we're going to fight Alduin at the start of the game, so I really don't see the main quest ending too soon being a serious problem, the only way that would be a problem is if the main quest is just too short. In any case, trying to introduce parts to the story after the epic "final confrontation" against the main villain can be a dangerous move, as they often turn out to be much less satisfying, for one thing, it's kind of hard to hold the momentum of the story once the main antagonist is already that, and it's rather hard to introduce a threat that can top a literal god, and once the protagonist has already succeeded in defeating said god, it can be rather difficult to capture a sense of drama with a lesser villain, so I'd say the main quest should just end with the defeat of Alduin, maybe there can be some brief events afterwards, such as a quest to escape from the location of the final confrontation, or serving as an epilogue to the events that already happened, but it can't be too long or I just start to feel that the game should be over already. End the main quest where it should end and just lwt me keep playing to potentially do other quests after it's over, that would be enough for me.
How can the main quest continue...if its completed? That's a contradiction. And some of you are assuming way too much. We dont even know if Alduin will return, or if we stop his return, or what. So speculating on zero information is simply wasting time.
Considering that Alduin's goal is to eat the world, destroying the current one in the proccess, it seems to me that we can logically assume that we MUST succeed in stopping him, after all, you can continue playing after the main quest, which would be rather hard to do if the world is destroyed, we can also presumably assume Alduin is the final boss, as he has been made out to be the power behind the crisis in Skyrim, therefore, it seems pretty reasonably to assume that we will have to deal with him somehow, that this happens near the end of the main quest as if we defeated him half way into it, everything after that would seem trivial by comparison, and that we do succeed in stopping him. How though waits to be seen, though I'm expecting an epic final boss fight of some sort, after the criticisms of Oblivion's ending, I don't think Bethesda will make the mistake of having the day saved by another character summoning a deus ex machina again.