Yes they did say the framework was a distributed system so it can never be destroyed although Aida should be able to shut it down if she wants to.
Watching the episode I think one of the things they are setting up for is the return of Ward. My reasoning on that is Fitz realizing he is Ward. That all it took was being raised by an evil man and hooking up with an evil woman to make him evil too. So the members of the group who would never have accepted the return of their black sheep will be more open minded about it. But I suspect it will be like Bobbi. He and Tripp will both wind up returning but will be off somewhere else and make occasional guest appearances. Maybe they will become part of Bobbi and Hunter's team.
I have said this a few times. They have the machine Aida used to make a human body. I forget if the machine was on the oil rig or someplace else, but even if it was destroyed - Fitz worked on it and could probably make another one. This would allow them to make real bodies for Ward, Tripp, Mac's daughter so he can have her alive in the real world, and anyone else.
Then just transfer their framework minds into the bodies.