Is there a way to upgrade a military station's defence platform?

According to the stellaris wiki, the answer is no.

The only alternate solution is to scrap the old one, and build a new one, in the same place.

Looks like we can upgrade stations now, as of the Asimov beta release. I am not sure whether this is new in Asimov or if it was added in Clarke, as neither set of patch notes makes specific mention of it. However it does say in the Asimov release notes that AI controlled empires and sector managers will now upgrade stations automatically.

To upgrade manually, select the station and click the upgrade icon. This icon should be grayed out if you don't have the resources yet. I've confirmed that automatic upgrades work for sectors as well, and is typically done very quickly.