I have installed the ERPoE for customers before. You can remove the ports from the switch interface. Attached is a screenshot of what it looks like in the GUI. Just uncheck the boxes, and those ports are no longer part of the switch interface. I could be wrong here, but it might be worth checking out before you dog your Ubiquiti equipment.
I've been using Ubiquiti routers, switches, and access points for over three years and they haven't failed me yet. The very router you're cursing I've installed for a hotel and uses VLAN's (I don't have any ports included in the switch0 interface). Their network is also running a 24 port managed switch and 12 UAP's. I've had two calls from them in the last 18 months, and one of those was to setup an OpenVPN server. Not to mention the 200+ customers at the ISP that I worked for who are using their various WISP technologies. ;-)
Just hang in there and you'll get it figured out.