Firstly I see no problems at all in playing in a Church,I can play a few hymns on my concertina and the Salvation Army used to have bands playing religious music.Surely it is how the music is received by the congregation that is the important factor.
Playing music in Church can offer problems however with sound, if it is an old church. I have heard a number of recordings recorded in church and the high ceilings create an echo, this is fantastic for slow pieces but with faster numbers the echo catches up with the music and creates a jumbled sound. Rather like playing two recordings of the same piece of music one about five seconds after the other. Some like this effect and with slow numbers it can be very moving, but is annoying to me after a short period of time.
Al