3) Let the group fight the Dragon by his lonesome then leave, probably in triumph
I vote for option 3
Where did they take their long rest?
in my game the PCs also cleared out everything aside from the Ettins (who they made friends with ) and the Dragon.
Whilst they rested in the entrance of the cave, I felt that now that the influence of the cult was gone that the lair would return back to what it should be. I took inspiration from the Green dragon lair entry in the Monster Manual.
So the Party heard the sounds of nature returning back to the lair, but unless they wanted to sacrifice their long rest to investigate they would have to leave it alone. 8 hours seemed just long enough for it start happening for me.
Also meant that if the PCs wanted to return back into the lair they would find that the easy route back via the rooms the cult used was now full of vicious plants. If they head back that route then the dragon will be aware of them and can be prepared. Plus dragon can always escape via the pool and leave the cave to fight another day, leaving treasure behind so they can feel like they have won.
hope that helps