Typically it's the opposite. The more of the main quest you do, the better ending you get. So I wouldn't worry in this case.
Like, if you defeat Ganon but don't have the Master Sword, it might mean that he's only gone for a short time and not sealed away, but if you go through the main quest and restore the Master Sword, he is much deader/sealed away for good (obviously not for good, this is LoZ after all).
Yes, that definitely makes sense. And would work for me.