Huh, Bookkeeper reminds me of my Assassin, in that it will usually be a Militia/Ghost Ship mashup that always hits you the most unpleasant. Your approach is much more elegant, though, because as you said, it doesn't cause sequential decisions. I'm not sure whether you underestimate how harsh the attack is - less cards than Militia, but can't be shrugged off. Not that i can really judge it.
Edit: Oops, didn't read TheOthin's post before.
Edit 2: One should also compare it to Bureaucrat, which it actually seems inspired by. $2 are pretty on par with the Silver gain i think, but like with Militia, Bookkeeper never fails.