Would an atheist be a better leader? In my opinion yes, but cannot prove it. What I'm sure about is that being educated into not questioning beliefs imposed from above makes people more easy to herd by bad leaders. I wish someone could do some independent unbiased research in this field, then make sure the results remain independent and unbiased even after publication.
What I've struggled with for a long time is the realization that the person I was, believing all of that, wasn't some brainwashed religious nutjob. I was just as 'rational' then as I am now.
Even worse, if I'm fully honest with myself the paradigm shift wasn't primarily a result of my own rational thinking, but significantly affected by social issues that made it hard for me to keep sweeping various realizations under the rug. If not for the non-rational issues, I might've still been convinced born-again evangelical christian.
I don't think that, day to day, an atheist is a better leader than, say, a born-again evangelical christian. In my experience the quality of a leader is largely unrelated to the 'paradigm' they buy into. There are so many aspects to being a 'good' leader that are entirely unrelated to the version of reality one ascribes to.
Where I /do/ think there's a really issue, is that by and large born-again evangelical christians are less 'anarchic' than atheists in their approach to leadership, and that they tend to operate in environments that are more homogenous. So it's possible that a terrible evangelical leader gets away with it because they keep moving within a very homogenous environment.
but I'd argue that this problem is possibly just as much the case with particular SV-style leaders. Or C-level people in a broader sense. I more than once felt that the processes that led to certain people occupying high-level positions in the companies I worked it were not that different from what I experienced back when I was 'in the fold'.
Perhaps it's not the same, but I'd definitely argue that it's a blind spot for 'atheists'. The idea that somehow they are not as susceptible to the dynamics of, among others, the Evanglicals.