Do separate VLANs behind the different SSIDs provide protection?
Inter-VLAN routing shouldn't be done at the wifi access point, packets would need to be tagged coming out of the wifi AP and switched upstream, unless I'm mistaken about this.
But yeah I agree, generally it would be receive traffic on a bssid, tag it, and send it out the wire upstream and let the switch deal with sending it back if its allowed by whatever VLANing policy you have.