I think that it is being established that the TVA is not a benevolent organization. Even if the rank and file are being tricked or brainwashed, I think that the Gobi Desert and France scenes are actually quite sinister. Fixing the timeline kills everyone on the new variant timeline. As Mobius euphemistically tells the French kid, "We are going to get you back to where you belong."

I think Loki helps defeat the variant Loki or Lokis and then realizes that they were in the right, and also that he does indeed have a purpose beyond ruling, and that is to free people from the tyranny of the Sacred Timeline.

This, coincidentally, proves Mobius right about Loki's penchant for destruction, and him existing to make others become their better selves, as this will have an affect on the heroes across the next phase of movies.

Also, interestingly, the variant Loki or Lokis are doing the same by making our Variant Loki realize his full potential.

Sadly, I don't know if anybody will realize the sacrifice that Loki made. Though, the wildcard in this theory is, does Loki try to establish his self as the God of the multiverse...but that seems a little TOO comic booky for the MCU, even if they are trending in the direction of bonkers stuff like that.