1) When the Earl almost recovered the Akuma Egg, he tried to countermand the order to destroy the egg, presumably to instead order the Generals to try recover it despite the risk of the Earl stealing it back, but reluctantly gave up when told it was impossible.
2) He took Lenalee, a potential heart candidate, to Helvaleska to have her innocence put in forcefully (a process that had never worked and might create a giant monster) while the level 4 akuma was rampaging through the order, chasing after Komui who was also going to Helvaleska. With every other exorcist incapacitated by the level 4's initial scream. That was insanely risky on so many levels. And he had no way of knowing whether Lenalee would be able to stop the level 4 even if she did synchronize. Don't forget that he was also risking his own life - if anything had gone wrong, he'd be at ground zero, unable to escape. The safer action would have been to do what Hevaleska asked, take all the Innocence and run to the Ark. In the end, his chance-taking paid off, but it was a close thing. Say what you will, but Rouvelier clearly has balls.
3) Cross probably told Rouvelier what Allen was long before he reached the new headquarters, yet he was willing to wait until Allen had made the gate before restraining him.
So, not freaking out just because Allen is actually a Noah seems very much in character. Currently he has a Musician to operate the Ark who he knows is not currently a traitor, and who could potentially serve as good bait to lure the Earl into a trap. Best case scenario this will eventually become a person who shares Rouvelier's goal of destroying the Earl and has first hand knowledge of how the Earl operates. Worst case the 14th wakes up surrounded by exorcists who can mob then restrain or kill him.
No wonder why Rouvelier's been looking so pleased.
Also, this seems obvious to the point that I suspect I'm missing something. The sword created when Allen goes over his limit is supposed to kill a Noah without killing the human host. Couldn't he, like, stab himself or something? I suppose this could backfire as stabbing seemed to make Tyki's Noah even stronger, but Allen's innocence is inside him all the time. Maybe it's evolved or is evolving into a form that can protect Allen from his Noah? Just a thought.