When one of the major games media outlets (Fox-owned, ironically) does something like this, we can let the politicians and cultural hand-wringers frame the discourse for us...or we can do it ourselves.
Removing the video and saying you "crossed a line" is a woefully inadequate response. You need to issue a formal public apology, and the people responsible for creating and posting this video must be held accountable. Jack Thompson is the least of your worries. You need to answer to us, the gamer community, many of whom resent the self-inflicted black eye you just gave us.
Step up and do the right thing. Until you do, I will no longer visit your site, your sister sites (Gamespy and Rotten Tomatoes) or your podcasts. I encourage others to consider doing the same.