Oddly, I'd have to class this puzzle as simpler than you expected. It's just a variant on "Speak, friend, and enter" from Lord of the Rings.
And everyone should know that? The type of puzzle is separate from the fact that it was a situation that the player had to deal with who may or may not know puzzles and it is the character that suffers the consequences. That's not a good mix for the game, even worse when its a matter of life and death.
The critical part you missed was looking up Wrath and Justice in the Bible. Instead you went for unrelated physical characteristics of the book itself. Expecting a player to look up Wrath and Justice (maybe finding an iconic verse about either) is not out of line in the slightest.
Actually, it could be
way out of line. Religion is touchy at best and forcing someone to look up material in any religious text as a crucial part of a game is seriously out of line unless the DM and Player both have discussed it ahead of time. If the Player doesn't mind and likes a Sunday School lesson thrown in with an rpg, that's about the only exception to it not being out of line.
Or you can role-play it, but if you're not clever enough to see the answer, your character dies.
That's not roleplaying. There's no interaction between the character and anything at that point. For that puzzle it was the Player having to solve it (or not, in this case) and the DM killing off the character because the Player--not the character--failed to solve it. The character was well trained on the subject of Religion and should have had no problems solving the puzzle, the Player, not so similarly trained, failed. Ability/Skill checks should have provided signifigant clues about solving it and the DM should have known that the Player does not have the same training as the character and cannot do the things that the character in game could do. Clues could have been provided and hints given to lead the player to the correct answer. That would have demonstrated some value in the character's religious training (as well as allowing the Player the chance to use that skill with meaningful results), and would have been more satisfying helping him along so he could come to the answer himself; rather than just giving the answer for a good roll, or outright denying it because the Player did not have the character's knowledge.
The DM's complaint about whining is way out of line. What did she expect after putting her Player through hours of an obviously opposite-of-fun time? She should consider herself lucky that 'whining' was all there was, and be happy if her Player gives her a second chance at running a game.
In my opinion you just lost patience too quickly...The riddle did make sense
That is easy to say in hindsight. Maybe you would have done better in his shoes, maybe not. But the point is, he did not, and there's no excuse for the DM not picking up on that and moving forward. Player's rarely possess character knowledge and when they don't it's up to the DM to be that knowledge and provide clues/answers that the character, not the Player, would know. In D20, I read somewhere that 4 ranks in a skill is about the equivalent of a Bachelor's Degree. If that is true, and based on the stakes involved in the game, the character should likely have been one of the foremost experts in his field if he had around a +10 modifier or whatever. The character would have been able to solve that puzzle in minutes, if not sooner!