Completely natural though it only bugs me if it's an incestuous name like my brother's or my father's and definitely if he goes by my mother's name, yeah, that's a deal killer.
So I think your feelings are valid but then his other qualities might determine how you deal with it. At least hang in there one more date and I'm certain you'll find five other reasons your critics will agree acceptable.
While it is true that you can compartmentalize thoughts, it's bullshit to think that not one iota of that won't leak through. So if he had my name, well, weird but not a big problem, it would save on monogramming. A friend's name, not a problem. The name of someone who had hurt me? That might be a problem. Depending on the leak, sometimes you bail, sometimes you abandon ship.
Learning that a guy has that familiar of a name is like reaching into his pants and feeling a cockring or a PA. Ick. So for me, in theory, that's just too distracting. In practice, I've only come across that situation--the name, not the cockring--once and I did go on that second date and that name was foreshadowing, be that my imagination or not. He was a nice guy, but still, my initial hesitation fit the situation.
You don't want to confuse one thing for another but you do want to be able to read into all of life and names have meaning to me. Certainly there's no reason to have to expend energy on detrimental associations be that an abusive person or even the associating of intrusive thought. Why dwell in that reminder?
I had a command for wolfpuppy when I wanted him to avoid something I thought bad: "leave it be".