I never thought it was that difficult a plotline to reconcile with the character. Actually I thought it explained a lot, his forced over-the-top behavior and awkwardness early on can be seen as him trying to play a "normal" human and failing miserably because he's isolated himself and become anti-social to keep his secret.
It also gave the writers an inroads to create the whole Section 31 thing. It would've been difficult to pull off without some good reason why 31 would want him.
I suppose I can see the actor's agitation, but at the same time, it's a sci-fi series. You should probably expect a weird development or two every once in a while. Siddig comes off as whiny here, IMO.