Pretty much how I felt. Not to bring up the dreaded FG vs. AD comparison again, but that AD episode was about tolerance and acceptance, a much better message. This was about conversion. Brian could've easily just convinced Meg that book burning was wrong instead of convincing her that God doesn't exist.
Sort of an aside, but I don't think all the blame for Brian's dialog/beliefs should be placed on Seth only. It's very possible that there are other atheists on the writing staff who want to soapbox their beliefs through Brian's mouth.
As for the Next Generation plot, it had its amusing "real life conversation" moments (such as the McDonalds drive through), but it didn't really go anywhere.