Well, real nuns indeed don't wear pastel-blue or pink veils.
I see people bringing up the existence of angel and demon Digimon as an argument, or how that they're Christian and not offended. However, that's a very skewed comparison. Nuns are actual real-world "professions," unlike angels and demons. Also, I doubt that practically anyone arguing about this are nuns themselves, so why can they speak for the nuns?
Not that it justifies the censorship in the first place. I'm against censorship, personally. Just pointing out that those are unfair arguments.
Maybe this is a bit tangetial, but I looked at
the Wikipedia article for The Da Vinci Code, and the biggest backlash did
not come from Opus Dei, the organization depicted in the movie and novel, but various other people. (Opus Dei complained about it, but they weren't involved with the protests and bans)
What I'm trying to get that is, this kind of uproar (when it actually happens) seems to be about the religion itself general rather than the specific religious groups actually portrayed.
Also, the "depicts a real-world profession" standpoint just gets really weird when you remember any other wacky thing in mass media. You can find analyses on how basically any profession is portrayed wrong in TV shows or whatever, and all of those are far more direct than "a monster that dresses like that job".
Perhaps more relevant would the old D&D Satanic Panic, which had more to do with allegedly being "occult", rather than say, clergymen complaining that the Cleric class was a bad portrayal of their own job.