This is a complex question, because there are many perspectives. In other words, what is too much control for one person is not for another.
First, it should be stated that the church wanted to have a lot of control. Just like the Protestants who settled in Massachusetts, the Catholics wanted to create a utopian Christian society in modern day Canada. They wanted to, in a sense, start over and create something from the ground up that was distinctly Christian. For this reason, they sent many Jesuit missionaries not only to maintain Christian principles, but also to convert the native population. By 1642, the church was the dominant force in Montreal.
Second, there were may setbacks for the church. For this reason, their control was not as great. For one thing, they often fought with the native population - the Iroquois. By 1650, the Jesuit mission was almost completely destroyed. From this perspective, the control was not too great.