I am maintaining the Pacifist mod which removes all kinds of military stuff and biters from the game.
Milestones handles that rather gracefully in that it does not crash, but it gives big red warnings that it had to remove milestones about military science, worms, etc. And it contains the list of kills that never kan be reached as there is nothing to kill.

I would like to programatically remove those milestones, is that possible?

Yes, you would want to implement a preset for your mod, which would be loaded instead of the Vanilla preset.
Check out the "I want to add a preset for my mod!" paragraph in the mod's main page.

That means I would have to make copied of most presets existing presets that include biters and/or military stuff. I'll have a look.