So a TV Exec at the time reads the draft ...
The decision for the wedding to be set in a chapel was by Paul Schneider, the man who wrote the script. To show Angela Martine genuflecting prior to the ceremony was either in the script, or a decision by Vincent McEveety, the episode's director.
Entirely speculated on my part, but given what I know about the time and circumstances very likely.
It's difficult seeing it happen the way you laid it out. Again the script writer put a chapel scene in the script, the art department recieved their copy of the script and redressed the briefing room to be the ship's chapel. Removed the big table, brought in benches, built a small platform and podium. Matt Jefferies (art department director) would have designed the multiple religious symbols on the alter, and the layout of the chapel itself.
All of this would have been directly approved by Gene Roddenberry. There not a chance in hell that he was "out of loop" at any point.