This used not to be a problem because I was loading all my js in the footer, but then a WP update broke the footer js enqueuing, so I had to make do.
Since I can't trust WP to not break their own CMS on update, I'm not personally wild about making my plugin use whatever random version of jquery/ui they decide to use that week. It's much more important to me that my plugin work across many WP 3+ versions, because in the past I have seen many sites skip WP updates due to some new critical issue they've created in the 'recommended' release.
Also, I'm only affected enqueued/registered jquery/ui versions on my pluigin's admin page, no other part of the site should ever be affected. I consider this a completely reasonable solution to my problem of having to refactor my plugin for every WP release.
I welcome other tested solutions if someone wants to try something differently.
Currently, I have a completely fresh WP 3.5 install w/ QW 1.5rc6 and it works in FF and Chrome. But since others are still having issues, I'm going to try the following things.
1. I'm going to try putting it the js enqueue back in the footer
2. If that doesn't work, I'm going to see if I can make small changes to my JS to allow it to work correctly in WP 3.5 and ~ 3.2.
3. If there is not a simple method that will work on both WP versions, I'm going to completely strip wordpress's jquery/ui from loading on the query wrangler edit pages, and hardcode versions I know to work.
In future versions of this plugin, I plan to drop the admin tabs UI and focus much more on replicating views UI specifically. Having to support 1 js heavy interface should be plenty.