I haven't seen the movie.
I don't have a problem with the idea of Section 31.
It's like acting like Western Nations don't have things like the CIA and Black Ops, or that Britain doesn't have the equivalent of MI6 or SAS.
They do things that we like to pretend don't happen in order to continue our way of life, and to continue our illusions that it is through superior ideology that we are able to practice Western Ideals and morality, rather than the idea that these things are protected by those who do dark things to protect them, rather than the world merely respecting them and allowing us to keep them.
However, keeping the things they do in the shadows is probably important.
Even in DS9 (if I remember correctly), though morally it was wrong, ultimately it was Section 31 spreading the virus (or disease or whatever it was) to the Founders is what won/ended the war, even if it was done via offering a cure via Odo and the solution was found in a round about way. It didn't end how they envisioned, but it DID play a key part in preserving the Federation.
In that way, I think keeping Star Trek idealistic, but also being realistic about the fact that such ideology does not exist in a vacuum, without those to do things that are counter that ideology in order to preserve that ideology, the chances of a morality of that sort surviving on it's own grows dimmer.
The same as our own Western Values (whether you see that as a good or evil, part of the reason we can keep and preserve them are due to the dark things others do in the shadows to preserve our way of life).