Joe, you raise a very interesting and multifaceted issue in your post.  I do not feel that there is one precise "solution" to the issue, but I will share some of my thoughts on its complications.

Due to the fact that the religious non-profit is performing a secular function that is not necessarily directly related to Church doctrine, I do not feel that the involvement of the Massachusetts government is inappropriate.  Unless the non-profit seeks to place children in specifically Catholic homes, I think that the government's involvement is permissible and perhaps even desirable as yet another means of ensuring that the children are placed in a safe and healthy environment.  

Furthermore, I believe that the non-profit's decision to cease its adoption program could certainly be construed as an act of discrimination against gay couples.  As the group is certainly entitled to its religious beliefs, it seems that the primary issue is whether placing children in the homes of gay couples would constitute an absolute violation of Catholic doctrine.  In my view, placing these children in such homes would be permissible so long as the homes were deemed to be safe and healthy environments by both the non-profit and the government.  Nevertheless, it seems that perhaps the non-profit would be unwilling to consider the home of a gay couple to be a healthy environment for a child.  Needless to say, this point of contention is both debatable and potentially volatile.

In any case, it seems far less debatable that Newton does seem to exhibit a certain wariness of the Church's potential intervention with regard to his work.  He seems to portray himself as a defender of scripture, as evidenced by his comments on relative quantities:  "Furthermore, they do violence to sacred scripture who interpret these words as concerning measured quantities there" (27).  I assume that we will be discussing Newton's religious beliefs, as well as his interactions or conflicts (if any) with the Church in class.