The look on Alastair's face made him want to apologize profusely and promise he did believe him. Charlie didn't ever want anyone he loved to look at him like that, with hurt and betrayal, but he didn't know what he was supposed to do. He had to know. If she was his reason for being in the Order, he'd understand, but he wouldn't be able to be with him, as painful as that would be. He didn't want to be used, even if it got Alastair access to better people. He really just wished the other man had just trusted him enough to tell him the truth so he could have been helping from the start.
"There is nothing I want more than to believe you, I want to believe you so badly, because I don't to live in a world where I don't feel like I trust my best friend to tell me the truth." Charlie could feel himself start to get defensive and he actively worked to keep that out of his voice; being defensive here wouldn't help either of them, wouldn't save even their friendship, and definitely wouldn't keep Alastair in the Order and Delilah safe with them. He felt like there was a lot more going on than just their romantic relationship, but they'd gotten to this point and they couldn't take it back.
"But I apparently can't tell when you're lying, Alastair, and it is killing me because I don't want to doubt you, or us, because I love you and I...I don't know what to do with the fact that you didn't trust me to help you get out of this in the first place."