I don't know. I just finished the game. And I'm also not sure any of what I'm about to type will make any sense, as I haven't had time to give it much thought yet.
An individual's reality is just a matter of perspective. Yes, in Trip's reality all of these people were captured and forced into a virtual reality. But that was no longer the reality of the people hooked up to the masks. They lived in a different reality that was apparently all rainbows and sunshine. It wasn't fake to them. Was it right of Trip to decide that their reality was the wrong one? Not really. But it wasn't right of Andy Serkis to force them out of their reality and into his either.
But what I am curious about, were they really "forced" into this reality? Yes, they were kidnapped, but we were never shown if they were given the choice of the new reality or not once they got there. I mean, when Monkey is given the mask, he seems genuinely content and doesn't resist at all. Were they really slaves, or not?
I think Trip's decision was more about her own personal vendetta against Pyramid for killing her father. Which is understandable.
Also, while I love Trip as a character, she was perfectly okay with "enslaving" Monkey for her own ends, but when Pyramid does it he is evil?
I don't know. The ending is left purposefully ambiguous. And it kind of makes me mad. Would even a little closure have killed them?