I wonder if Framwork Ward is actually a good guy, or just his obsession with Daisy makes him want to protect her.
Ward always believed he was the good guy, or at least that he was doing the wrong things for the right reasons -- reasons that were mostly personal and driven by his need for approbation and love. When he was a Hydra mole within SHIELD, or a Hydra leader working against SHIELD, he still loved Skye/Daisy, wanted to protect her, and hoped he could convince her to see things his way. It's perfectly in character that, in a world where Hydra ran the show and SHIELD was a subversive group, Ward would still play both sides in the interest of protecting Skye. He hasn't changed, only his context has.
Maybe I'm forgetting something, but I assumed the reason why Simmons was dead (and not in her happy place) was because the framework wasn't adapted for her. She and Daisy just took over their avatars, wherever they already happened to be.
I'm not so sure. In the closing scene, Aida/Madame Hydra said that she'd closed off Simmons's avenue of escape, and in the earlier scene with Jemma and Daisy, Jemma said that the escape beacon didn't work because it was connected to them and her death in the simulation had changed the coding, or something like that. So it seems like something Aida did on purpose.
One has to wonder about the larger implications of the MCU. Did 'The Incident' still occur? Was the Avengers Initiative still a thing? Is Rogers still on ice? I assume Project Insight went off without a hitch, so Fury, Stark, Strange and Banner etc. are probably all dead.
If SHIELD was discredited and Hydra took over due to an incident in 2008, then Project Insight would not have been necessary in 2014. As for the Battle of New York, since the Framework is supposed to be a safe, idealized world, I'm guessing Aida programmed it to be free of alien threats.
Remember that they are non player characters, lines of code and presumably Madam Hydra as the game's master wants Simmons to have a productive happy life in the framework.
Again, the last scene gave the impression that Aida/Mme Hydra's goal is to keep Simmons and Daisy from endangering the Framework by escaping. She cares more about the survival of the Framework as a whole than she does about the well-being of individuals who are trying to destroy it. Your classic machine-logic optimization algorithm, aka "The needs of the many outweigh the needs of the few."