Ya could make it similar to the bashing rule, only X number of successful MDs per account per day (or two days)
Or could make it tied to a players Astro lvl (so will roughly scale with points) like can only pop 25% of possible moons, so if a player can build 12 planets you could pop 3 moons per day (again numbers can change)
Like other said if you are watching a target and doing the research popping all moons shouldn't be needed and honestly is toxic play and causes players to quit IMO
While this doesn't directly address the cost associated with MDs like the original topic I feel this would accomplish roughly the same goal