Take the job.
You wanted the position, and it manifested. You wanted to be a better employee than Bob, and you are, your manager wants you running the show.
If your issue is guilt there's no place for that here. Guilt is the opposite of empowerment.
There's no reason to feel bad for getting what you wanted and deserve. And there's no bad karma that i can see in this scenario unless you intentionally screwed over Bob somehow.