Port cities of the middle colonies became bustling community centers because trade was very important and happened there. Many of the merchants lived in Philadelphia or New York City.
The role of the proprietors was too watch over the colony send more people and resources but it seems the english government would always take the colonies and say you are unfit we now are the rulers of this colony.
Saint Thomas would most likely said that the only reason he conducted the 'homophobic actions' was because it violate the rules of God.
In that time, this kind of defense was perfectly plausible since the Church at that time had a huge influence in the Government. But our time, this type of reason wouldn't be plausible.