I think the stock rims are pretty good. I've had a (blue) Xootr Swift since December 2005 and have over 1000 commuting/shopping miles on them without a problem. If you're going to be going fixed I'd think they'd be less an issue of sidewalls wearing too soon. That's definitely true of the rear wheel if you decide not to use a rear break.
As for the conversion, have you thought about the Surly Fixer, described in this pdf download from Surly? You wouldn't get a dishless rear wheel, but the 20" wheels are really strong as is. Also, I'm not sure if it would work with the Quando rear hub on the Xootr Swift, but if it would it would be an easy way to go without too much time (cutting out the orignial spokes and building a new wheel) or money (new hub and spokes).
Jonathan