This sounds more like a problem with the player than the character to me, try to remind him "this isn't what astartes do really do you want to do this?" when he draws a weapon for no reason in front of the Emperor for all intents and purposes
Something I occasionally do is give the PC a roll of, for instance, common lore adeptus astartes with a big bonus. Then, when and if he makes it, you (the GM) tell the player his character knows he is not to do this. That will give you an idea of whether the player is jerking you around. In SOME case, and I'm not saying that is the case here, players are unfamiliar with the way things work outside of a video game (actual roleplaying) and need to nudged along. I believe that is for the GM to decide.
Regarding getting in a fight with the keeper, should the keeper have realized how the librarian intended to use the force sword?