The RM Amazons are not relevant for the use of Roman temples, be they from real history or the history of Mythic Europe.
Temples were indeed not churches, but they protected sacred images and treasures. Just opening or closing the doors of Roman temples could have special significance. See: en.wikipedia.org/wiki/Religion_ ... nd_shrines .
Cheers
So they basically used the "Don't interact with each other in person" trick the Soquotrans use. It works for those guys because they don't need to interact, but the Cult of Mercury definitely did need to do so. Presumably the upper echelon of the Cult was comprised of Gentle Gifted, who would both interact with the Roman authorities as well as co-ordinate groups of wizards (ritual leaders). If I was running something like that, I'd make sure the wizards never were able to identify each other during cult practices (masks and hooded robes galore), and maybe make sure they were getting a good buzz on something before the gathering. 
Is it well established that the magi of pagan Roman times were subject to the unsocial penalties of the Gift? Citation?
I am not aware of quotes explicitly positing the Gift and its penalties in pre-Christian (i. e. BC) times. Heron's disciples, who by AM p.77 had The Gift, lived in the 1st century AD and later.
Magi entering the Garden of Eden (AM p.20 - but see also the box on that page for eventual further Edens) lose The Gift and the ability to work magic. And intelligent beings eating from the Tree of Knowledge there gain The Gift (p.22) - linking it to original sin. This would just hint to the The Gift existing since the fall of man, well before the birth of Christ - but it depends on the saga, what PCs make from such a hint.
Amazonian society (RM p.13) is older than Rome, and by RM p.15 recognizes the Gift. Since there is no written history of the Amazons, this may not convince scholars from Mythic Europe, though, that the Amazons found Gifted girls throughout all their history.
Cheers
Already quoted above from pg9 of the Core book. "The Order's History" highlights that the effects of the Gift were a problem for practitioners of magic from the 'beginning of civilization', and it calls out the Cult of Mercury as having these very difficulties.
Seems fairly definitive! Pop goes that idea.