I don't like anything reducing the Doomsday counter either, it just seems like it's gaming the system too much.
Another idea could be a Stasis-type spell: spend some mana to stop Doomsday gain for X number of turns (maybe influenced by # of shards) but at the end of the spell effect, the Dommsday counter jumps by double what it would have during that time.
Either a solution like those, or the reduce doomsday spell should be the special ability of one of the Sovereign classes.