I've been following FT threads all summer hoping to find an answer, and so far no luck. I'm including my info here to show the OP isn't the only one experiencing this. If you google "facetime disconnects wifi" you'll see there are several threads on the official Apple site, here and other sites with users experiencing the same problem.
I've been overseas since April and try to FT with my wife almost every day. She is using an iPhone 4, not jailbroken, latest firmware. I use my iPhone 4 or my MBP with FT. Nearly 100% of the time our calls disconnect in <10 minutes with her phone losing connection to the wifi and losing her network IP address. She has to wait for the wifi to refresh or manually cycle wifi in settings to regain connection. Neither my phone nor my MBP ever lose wifi connection--it always happens on her end.
Like the OP and many others, I think the issue must be related to her specific phone because she can watch a 2-hour Netflix movie or perform countless other tasks without ever losing the signal, and the problem never happens on my phone. We've also tried switching the Trendnet access point to G only with no success.
We don't have a nearby Genius Bar to try--yet. There's a store opening this month so maybe she can try them when the store opens.
In summary, this post is a very long "me, too," added to show that the problem is real and unfortunately has not been helped by the summer's software upgrades.