There are some misunderstandings regarding the position of the Grand Orient of the United States regarding freedom of conscience. Of course this idea provides for the admission of atheists which seems to be a bone of contention for some. This also allows for deeply religious people. The Grand Orient in and of itself is a non-dogmatic organization. It promotes neither atheism or deism. It is a secular administrative organization.
That being said there are certain rites of Masonry that lend themselves well to Brothers who are atheist. The "Restored" Modern Rite for example is one of these rites. The Rectified Scottish Rite on the other hand leans a great deal more towards a mystical outlook which an atheist Brother may not be comfortable with.
Within the Grand Orient both hypothetical lodges could exist side by side. The secular nature of the central organization permits a vast diversity within the organization. One lodge could be wholly mystical in practice and outlook while another could be entirely secular in its works. The Grand Orient itself takes no part in that decision.
Freedom of Conscience does not encourage nor permit anti-social or dangerous behavior. The fundamental foundation of Free-Masonry prohibits anti-social and behaviors that are damaging to society in general. Those prohibitions are actually a part of a social contract to which all citizens do (or should) adhere to. Without this understanding and respect for the rights of others society tends to decay. It is necessary for one to be unhampered by dogma in order to explore and grow.