Well, Beethoven was somewhat of a womanizer and that piece has nothing to do with religion or church. In fact, it's called "FOR Elise" in English. So, basically, you're playing a piece in church that's dedicated to some chick and was written by a womanizer. Maybe that's what she has taken issue with? Why don't you play something by Bach instead? That would probably be more appropriate for church....
And, please note - I love Beethoven's music.