I recall the logic of the note being along the lines of: "You're saying nasty things to me. I see that you're a Christian. How can you do this when being hateful is against your religion?" It read to me like a snarky response calling him a hypocrite (even if you didn't explicitly label him as such).
I have serious problems with this for a few reasons:
First, as a business owner, I don't think an employee should be anything less than the pinnacle of politeness when dealing with customers (which is what FB's users amount to - even if they're only paying you with eyeball time). Implicitly labeling him as a hypocrite was impolite. The note damaged my opinion of how FB is run as a business.
The second, larger, issue is related to privacy. Personally, I'm not comfortable with you treating my profile information as anything more than raw data - as neutral and uninteresting as a set of ones and zeros. Just as I wouldn't want my doctor to tell people things he knew about me, I don't think you should reveal information about this guy - either his religion or the impolite way in which he communicated with you. I seem to recall that information from his profile not being available to the general public.
Finally, when it comes down to it, his religion just had nothing to do with whatever feature request / bug report he was making. Just as I wouldn't expect a waitress to call attention to me having orange hair when I order a burger, I don't expect you to bring up my personal information when I give you feedback on your service.
Shortly thereafter, I quit using FB on a regular basis. I did so for several reasons, but that incident was certainly somewhere in my mind when I quit.