Right, it seems there will always be little nagging audio-related issues, often it has to do with the particular AVR you're using, other times it's trying to bend iTunes to your will, other times Apple breaks something with an update, remember all the reports of optical audio issues with the 10.6.8 update? Anyway, it's why a "home theater PC" is still a tiny niche, it all boils down to figuring out the best way to adapt to the other equipment in the chain, and in this case it's feeding analog to that Zone 2. Since you already have the USB out hardware, Lion's multi-output might make things smoother for you--but Lion itself might also disrupt something else in the way you have things configured. You won't know for sure until you try with your hardware--but before you install Lion, make sure you have a perfect bootable Superduper clone of your current Snow Leopard system, so you could restore it if needed.
This all works OK but only one audio output at a time is supported. The only real hassle is that after using the mini in optical out mode, it seems to require a re-boot to get the analog output from the USB adapter to work again. Not exactly a horrible situation but certainly inelegant. Seems to me that just switching the output source in Preferences should just work, but it does not immediately switch
Personally, I could never tolerate having to reboot, it would drive me crazy and I'd do whatever it took to work around it.
If you 1) weren't ready to try Lion, 2) were getting tired of your "inelegant" current setup and 3) were mainly interested in listening to music in Zone 2, I suspect if you ditched the USB out and fed your Zone 2 via an analog out from a wired Express, your experience would be much more seamless since it's actually officially supported, just toggle the Express destination on or off. Wired it would be much more stable, your iOS devices and other Macs would see it, and you wouldn't be switching per se, you'd be adding to your optical. I used my Express like this for years and was very pleased.
Regardless of what you try next, let us know how it worked out.