Interesting topic. Let's dive in...
It's true that Draper isn't as alpha as James Bond. His character arc in the series is huge as it starts him out as the man on top of the world both in his personal and professional life and slowly has him spiraling down as the series progresses.
However, I think you're nitpicking on a lot of the things he does. After all, he's human like the rest of us so not every move he makes is the correct one.
If you remember, he was raised in a whorehouse, so he's got issues with infidelity. The situation with the hooker was beta, but possibly tied to his past and how he was raised.
I don't think him wanting to run away with the Jewess was beta at all though. He thought that Pete would rat him out and he'd have to face serious jail time. While it makes sense from her perspective not to go with him, who could blame him for wanting to run?
If you look at the way Don holds himself, it's very alpha. He's always in charge, knows how to lead in a relationship, and is a very cunning businessman.
Compare him to Pete who is sneaky, jealous, talks behind people's backs, and cannot be trusted. He basically represents your every day man (or at least one in the big cities where males are ultra-competitive). Hardly a man to admire.
Now Roger on the other hand is classy, good with women, but not a leader. I think even Burt said that in one episode. Charming? For sure. But he's not the one you want in charge of things. So by definition, he's not a classic alpha either. He too is human, but with many alpha traits.
No man in this series is James Bond, but then again, what character can live up to those expectations?