[Gryphin]

gravey101,
If you like using missles, you may cossider giving most of your missle ships types "Do Not Fire on Planets",
Then build a few "Specialty" type missle ships that will fire on planets. As you noted, the ships fire weapons untill all of the threat weapons are destroyed. Since the missles have not reached the target yet, the ships continue to fire them.
The other option would be to build a few "Planetary Invasion Ships" that have direct fire weapons. In either case, it can be a logistics pain.
Enjoy