[Grandpa Kim]

The only sure way I know of to destroy planet based defenses and not the population is to land troops on the planet. Here's how it works in simul games.

Load up a transport with troops and give it "capture planet" as its primary movement strat.
Add it to a fleet with the same movement strat. Set every selection to break formation.
Attack an enemy planet.

The attack ships in your fleet will head to the planet and fire on it till all WPs with offensive weapons are destroyed. They will then either stop where they are or move away from the planet.

In the meantime, your troop transport, whether armed or not, has headed to the corners along with the auxilliary ships and won't come out till that Last offensive WP is destroyed. It will then head to the planet and drop the troops. (Note: Only one transport per planet per combat round will drop troops. A stalemate will allow a second transport to drop additional troops on the same planet in the next combat round.)

If the troops win, you have gained one intact, populated, facility laden planet. If the troops lose, alas, your fleet will glass the planet.

Exceptions: If the planet has a low population, say 10m or less, you may glass it anyway when the overage of the Last shot slops over to the population. Warning: Using missiles is dangerous and may glass much bigger planets.
If the planet has sufficient defenses, your attack ships may lose. The troop transport will then try to capture the still defended planet. Obviously this rarely succeeds.

The way I see it, the only reason to kill the defenses and not the population is so you can capture the planet, so why do it piecemeal; do it all at once!