I think Ed does kind of come off as more of a dick in the first two episodes of the first anime than in Brotherhood, but I think that's more of a problem with what the first anime, and by extension the manga, decided to show first. When we first see Ed talking to Rose about Cornello's promise, we know nothing about his past so it comes off less as "Stay away from trying to raise the dead" and more "lol you believe in god what a moron."
Also, the first anime is kind of anti-religion in general, even to the point of throwing in a completely unnecessary line about Christianity being a dead religion. Brotherhood, on the other hand, is much more neutral about it.