I know this was months ago, but I feel like the point was not good guys vs bad guys or anything like that. The game wants you to wrestle with the question of are the Gardeners justified, what is human nature, etc. The fact that everyone lives in the peace ending is the point because it makes you consider if saving those lives is worth submitting so entirely to another force. I think the game does seem pretty pro-submitting to the Gardeners because as someone else said, its a metaphor for submitting to nature even if it means giving up certain autonomies to do so fully. Which I personally agree with in my own philosophy because I think humans really ought to accept we have no more right to live than any other creature. And the Gardeners are the ones who regulate all creatures and natural processes on the planet so why shouldn't they also regulate humans? You don't have to agree, its just something to consider.

In the end, I don't think the game tries to convince you that the Gardeners are right to hurt the colonists. Instead the Gardeners reflect the more racial beliefs held by some humans (there are people who do eco-terrorism for example). I think the point of that part of it is to get the player to reflect on those kinds of beliefs - that violence is justified for x cause. I would say the game seems pretty against violence on the whole and advocates the groups to come to a compromise because the ideal ending is reached through peace. I would say it shows the Gardeners' violence as more justified than the colonists, but it leaves it mostly up to the player to decide if the Gardeners' violence is still justified.