Need Advice: Consequences for Players Disrespecting a Religion in a Story-Driven D&D Campaign

I’m running a long-form dark fairytale inspired D&D campaign where each kingdom has a major story arc tied to themes like corruption, faith, and restoring broken kingdoms. I use milestone leveling based on “restoring” a kingdom rather than XP.
My current arc centers around a winter kingdom ruled by a corrupted frost goddess analogue (this is a reimagining of the Snow White story with the evil queen as a head of a coven of witches). The party is working to restore the rightful winter goddess and save the princess/queen tied to her faith. Religion and divine themes are VERY important in this arc.
The issue is that several party members have behaved extremely disrespectfully toward the religion and the people of the kingdom during the campaign. Things like:
burning churches
damaging holy relics
antagonizing or mistreating frightened civilians/parishioners
stealing sacred fruit from a holy tree tied directly to the goddess (the apples that caused Snow White to fall into the sleeping curse)

At the same time, they are still progressing through the main story and are about to defeat the evil goddess and restore the rightful one.
One of my players (a paladin devoted to this religion) has roleplayed this very seriously and has decided his character would realistically retire after this arc because he would no longer travel with people who disrespected his faith so heavily. I actually think that part is great roleplay and world consistency.
My problem is this:
I feel like my players have started to assume that as long as they “finish the kingdom” and beat the boss, they automatically get the milestone level and rewards no matter how they behaved along the way.
I don’t want to come across as punishing players because I’m upset out-of-game, but I also feel like there should be meaningful narrative/divine consequences in a campaign where gods, faith, and morality are major themes.
Right now I’m considering:
delaying the milestone level because the kingdom is not truly “restored” yet due to the damage they caused
having the goddess selectively reward only the characters who upheld her values
giving the offenders some kind of fairytale-style curse/bane tied to the stolen sacred fruit
allowing the party to later redeem themselves and fully restore the kingdom to earn the level later

I’m trying to find the balance between:
meaningful consequences
maintaining player agency
avoiding DM-vs-player energy
keeping the world feeling believable and reactive

How would other DMs handle this?