could dr whale be a bad guy?

I don't think so to be honest. Just because you work for Regina doesn't always mean your a bad guy. Take Graham for example, even Sydney isn't truely a bad guy but both worked for her.

Also if you notice people's Storybrooke personas are often opposites of their fairytale ones in many ways. At their core they're the same but for example, Mary Margaret's very timid while Snow is forceful, and Charming is couragous while David is more of a coward.

Despite Dr. Whale's creeper vibe I actually kind of like him in a weird way believe it or not. No idea why to be honest, but yeah. Lol.

I dont think he knew who David was when he called Regina, so I dont read too much into that. Also, I did think he was sad when Henry died, and it is understandable that shock would be his main emotion when Henry came back.
That being said, I do think it is entirely possible that he is a bad guy. He is definately sleazy, and while there is no proof it wouldnt surprise me if he was working with Regina. The question is, is he just a perv, or is he a villian? Time will tell.

I do think it's possible that Dr. Whale is a bad guy due to his creeper status, but not from the other evidence you've given. We must remember that Archie also called Regina and betrayed Emma in the second episode. The residents of Storybrooke, before the curse was broken, had almost no backbone and were at the mercy of the mayor. She had her hands in everything, as Graham said. Plus, he's a big-time doctor. Patients probably died on him all the time. It's just part of the job. I wouldn't read too deep into those two things.

I've kinda been wondering if he's Captain Hook... but I don't really see the connection with his name or anything or that the blue fairy gave him a weird look when he was waking up. Besides that he was given a really high up position as a doctor, and he's obviously one of the people under Regina's thumb.