Neither yes nor no. The Bene Gesserit are a political organization, not a religious one.
Consider first that the Reverend Mother Gaius Helen Mohiam discusses that the Bene Gesserit focus almost exclusively on politics. This happens at the beginning of the first novel just before Paul is tested with the Gom Jabbar, and no mention of religion is made at all, only the juxtaposition against the Spacing Guild who had focused exclusively on mathematics.
Then consider Jessica's words in the first novel, given while voicing her concern for Paul's quickly waxing religious significance:
When religion and politics travel in the same cart, the riders believe nothing can stand in their way. Their movements become headlong - faster and faster and faster. They put aside all thoughts of obstacles and forget the precipice does not show itself to the man in a blind rush until it's too late.
Jessica all but tells us that religion and politics together is destructive. The BG, being one of the longest standing schools in the Dune universe, surely are not political and religious. They would have been crushed long ago.
Therefore, I posit that Herbert intended the BG to be a strictly political organization, where perhaps individuals may hold religious beliefs, but it is irrelevant to the goals of the BG. This further makes sense if you assume the BG legitimately believe they serve humanity through a sort of Paternalism. This would make them closest to Humanist, but without the apparent need to be Atheist.
I have little textual evidence for it, but it is fun for me to believe that the BG started as a religious organization (a Catholic order of nuns, most likely). It would be a great story in how they learned the harsh lessen that religion and politics cannot "travel in the same cart" and they were nearly undone. Something set many years before Paul Muad'dib. All of this pulls together for a more enjoyable reading experience for me.