Honestly though Allen is someone that can be suspected easily. He can use the ark which ahs been in enemy control for a very long time. He tried to save the traitor Suman whose actions caused the deaths of many people. Guy has a cursed eye that can see the akuma souls and he cares about them as much as he cares about people. Not to mention on the less known part he did intend to go and save Tyki from the collapsing ark before his Noah powers came back with a vengeance. Many like Chouji would see this kind of stuff as being traitorous and making him just as bad as the enemy they are fighting.

Wouldn’t be surprised about that Inspector causing Lenalee trauma. We know from flashbacks that she was forced to go to the Order and locked up/restrained. If her brother hadn’t come who knows what would have become of her mental state. Many of the exorcist friends she has have only arrived recently. Lavi came a while earlier but not too much. Krory, Allen, and Miranda are pretty recent arrivals. Kanda, Suman, and probably some of the marshals are probably the few that have had long contact with her.

In terms of Lenalee’s fate I have been thinking the same. You can’t just put out someone that is suspected of having the heart out there. Having it or not doesn’t make a difference. Long as the Earl believes she has it that’s enough to make her a serious target. If he is right and destroys her innocence then that is the end for them all. Besides the fact she can’t use it properly it makes sense to lock her up for now.