Yeah, the Desmond blackmail literally makes zero sense as of right now . I touched on it in my criticism, but the nature of his blackmail and the outcome of it makes no sense. The blackmail is meant to be a secret held by the holder about something in their past, so why would Eva assume the blackmail mean he had literal weapons on him as of right now? Not to mention it is one of the cryptic blackmails, meaning it could mean literally anything until you actively ask Desmond to explain it.
I will give some benefit of doubt and say they're planning on something later. In the trial, Desmond said he didn't even know his room had weapons, which has to be a lie considering the outcome of the trial, and, you know, logic. Maybe it'll come into more play later, but as of me writing this, it is a massive flaw in the writing.