This suggestion takes a page out of Helldivers 2 here. In that game, there are special locations in each operation that affect the map, but you are not required to destroy them.
For example in Helldivers, the automaton faction can have jammers that disrupt your ability to call stratagems and view the map. While you are rewarded by destroying these jammers, you do not HAVE to.
A simple example here would be the butler bots who repair everything. Maybe they are produced in a factory? Therefore, if I want my destruction on the city to be permanent, I have to destroy this factory.
This would be a cool way to facilitate natural goals for the player, while also demonstrating how their choices can affect the world.