I see that it is possible to configure the CSS classes used by tablesorter. So, you could change any of the defaults which conflict (though there aren't any that jump out at me).
I don't understand why there would be Javascript conflicts, since JQM is effectively in a namespace $.mobile
In general, though, my observation is that JQM is not very compatible with MOST standalone Javascripts, and MANY Jquery plugins. I think that many blindly plunge into JQM development without realizing that. JQM doesn't play well with others, primarily because of it's means of caching pages in the DOM. Unfortunately, that's a necessary evil.
Possible solutions would be a modification of the DOM across the entire industry, or standardization of page caching in the DOM.
