No, actually I felt it was natural to select him as the Governor. Those colonies were very religiously oriented (not the best way to say it) and he seemed like a very natural leader. Due to the fact that we saw only 8 hours out of 700+ filmed, and the personal tragedies that led to his family having to leave, I don't think you ever really got to see him reach his stride.
As far as the post interview and him saying it bothered him that some were leaving Europe to escape religious intolerance only to fall back into it here, I found that to be very interesting/signficant, however it's not surprising.
Consider this - he, a Republican/Conservative Christian, felt uncomfortable imposing religion on others (after all he wouldn't want it imposed upon him). Natural reaction for a true Conservative. We want to worship as we see fit, not as the State determines.
The liberal/democrat Christian, on the other hand, wanted mandatory church attendance for all. Some would defend him and say he was just trying to act the part of the 1620s, and they would be partially right. However, any sane/rational person would know that this would be one 21st century belief that probably shouldn't be touched upon too much. I believe he probably understood it was sensitive, but maybe he wanted to do some kind of personal study to see just how far he could push others in regards to religion. I don't know.
If this was a real colony facing real problems, I think Wyers, or Jack Lekza or Don Wood would have been much more capable leaders/governors than Heinz. Wood most of all. Besides the fact that he is a real carpenter and used to hard labor and and efficiency, he seemed to understand just what would have been at stake. He seemed like a better manager of people.