I think that it is very possible to overthink the situation and/or come to preconceived opinions about it.
I do not see Freemasonry at odds with my religion at all. It is a philosophical institution that, while spiritual in some aspects, makes no attempt to encroach on the domain of religion. I've heard and participated in several discussions on the topic and have heard many thoughts on it. There are a few "popular" concerns that most will cite, the above discussion being one of them (don't associate with folks outside your circle). Sometimes these come from uninformed non-members, other times from ill-informed members. Sometimes they come from well-informed members that have had a change of opinion on the matter.
Freemasonry is an idea, a philosophical teaching, a way of life; not a path to salvation, not a religion, not a substitute for God, church, or family. It seems to me a lot of the issues that arise with churches (besides straight up internet crazy misinformation, of course) come from not understanding this.