I have also thought of that, and I think it might be an interesting twist if that's what happens. But in that case, you can at least count on the Inquisitor most likely surviving.
My theory (and it's probably totally wrong because it's entirely predictable) for what comes next:
We might get Abelas in our party. IF SO, he appears to be working for us as a double agent, and it's unclear if he's working for us or Solas. Eventually we discover that he was working for neither, but for Mythal.
It's a game. Our goal is to stop Solas, either by killing him or convincing him not to do crazy stuff. And because it's a game, we're going to succed. We don't know all the plot and characters and places that will be involved, but we can count on succeeding, unless we're just a moment too late, or we can only manage to make Solas change his mind on the method, or something like that.
But, in-game prophecies tell us that the Veil is going away anyway. It's going to. We can't stop it. Thedas as we know it will end, and a new Thedas will rise in its place. The ancient elven gods are going to be freed.
Assuming I'm right and we stop Solas (because it's a game and of course we are going to win or what's the point in beating the game?), and it isn't just some fluke of last-minute timing that we just barely fail to stop him... who's pulling the strings?
Well, there are two possibilities, and one's far more likely than the other. The first is that Solas has followers capable of either working together, or as individuals, well enough that they can take over his plan. This requires that they know the full plan, and we know Solas is not very trusting. It seems unlikely. The second possibility is that Mythal, or Flemeth, or Morrigan--however she appears now--sees Solas not accomplishing the goal she set for him, and she moves to take over. If Solas is convinced to stop rather than killed, he will now be on your side in opposition to Mythal.
What would Mythal's motive be for this? Vengeance. And it might not just be against her killers (Dirthamen in particular possibly?). She said the world was betrayed. Solas could be the world's betrayer, or maybe it was the other elven gods. If it's Solas, he's in for a world of hurt since he trapped the pantheon and betrayed the world for her sake in the first place. Either way: her motive is vengeance. Whatever torment Solas is putting the enavuris through, it's not enough for Mythal. She will unleash them on the world, blinded by her own rage. And then we'll have to stop them with the next protagonist.
So when Mythal's hand is revealed, if Abelas is with us we will see him turn against us (even if he doesn't want to, even if he looks like a kicked puppy over it) because Mythal tells him to. Same will happen with Morrigan-who-drank-the-Well, assuming she is not Mythal, herself (in which case she acts against us because she IS Mythal)--we don't know if this will be the act of Morrigan or some other splinter of Mythal's spirit. And it will also become clear that the Inquisitor who drank the Well will now be pursuing Mythal's goals, and acting as she wishes. The Inquisitor will now be an antagonist against which the new protagonist must battle.
If you didn't take the Well, Abelas and Morrigan betray you. If you did, they don't, but that's because you're on their side. If you convinced Solas to stop, and did not drink the Well, he will now be on your team. If you did drink the Well, he will be your enemy (because you convinced him to stop and now you're doing what you showed him he shouldn't). It may not be possible to kill him. If he survives a more aggressive "stop Solas" effort, expect him to be your enemy if you did not drink the Well, and your ally if you did.
Only the Inquisitor won't be you anymore, if you drank the Well. No, you'll be the new protagonist who suddenly has to take down your previous protagonist. And that will be both deliciously plotty and horrible.
Will this part of the plot happen mid-game? End of game? I don't know. It's just a guess at any rate, and I could be very much wrong about it.
Just my take on what I think is to come. Again, it's simple enough that I am probably wrong. We will be thrown for a loop or encounter a twist somewhere, somehow, that we didn't anticipate. The plot might be something entirely other than what it appears that the plot will be.