The Scots were on the Parliamentary side in 1645, it was only in the second civil war (1648) and the third (1650) that the Scots disastrously took Charles' side. Scots were transported to the Colonies following the Battle of Dunbar in 1650, so that would date the ironworks to 1651 or after.

And, as you say, the prisoners were not in keeping with the religious atmosphere of the colonies- the experiment was not repeated, and thereafter prisoners went mostly to the West Indies. There is a sizeable 'poor white' population in Jamaica beleived to be descended in part from these.

I wonder if the ironmaster's departure was more to do with the politics of the time than to pique?