Jason, you could always do what other forum software does, which is that if a URL is over a certain amount of characters, then it will cut out the middle and replace what is displayed with ... and therefore you can limit the width that the page can be.
The other option is to do it EXACTLY like you did it in the version we were running before the downgrade, where ONLY the reply where the long link is posted causes the screen to require scrolling. I believe the reasoning behind this was "we load the table one row at a time, so the width is dynamic and it also allows the thread to be read as it is loading" (this also meant that rediculously long usernames looked slightly out of place, but at least the page didn't scroll if one numbnuts copy/pasted the longest URL in the world without adding some FT tags round it)
Garry