Comment 1 for bug 1222899

A reasonable work around for this is to make yourself a library footprint consisting of nothing more than a pad, same dimensions as your required via. In the pad details (in the footprint editor), set it to net GND. You can place that component anywhere you like and it will connect to the GND zone and not cause any DRC issues.

The only problem is it throws up errors about extra components but you can learn to ignore those.