My take on it is as follows: it was kneel. It was reflecting the fact that she came to pray in the first place, and she was kneeling when about to do so. He asked her to pray for him when they were in the vestry, and this was an extension of that. He wasn't about to abuse her, was just a continuation of the religious theme and them playing at Catholic confession.
He is a troubled soul from a damaged family and has put his past in a box - rather like Fleabag - to start a new life of abstinence and religion. Then he meets a mirror of himself, someone who gets him, and his faith is now challenged. Hence the drinking. Hence the continual references to his temptation and their chemistry: castration to avoid sex, her being turned on by calling him father, her being in his thoughts, etc. He's battling with it, and losing.
I think he's going to bottle it and move parishes. Sadly.
I literally discovered Fleabag last week, and it's the best thing I've seen in ages. I've binge watched up to the current episode and I'm gutted to read this is the last series. PWB has written a superb cast of characters that have great depth, and to captivate an audience with a relationship with so much chemistry in just 22 min episodes is a huge feat. Hot Priest has completely been in my thoughts all day, his mix of intelligence, vulnerability and quirkiness reminds me of David Tennant's Doctor Who, who I also loved. And total girl crush on Fleabag too.