It's nearly impossible to ensure someone's reaction to something you say/do. I agree that you don't want to hurt your friend's feelings, and that's a good goal, but ensuring her reaction to your statement is very difficult.
There are ways to express preference, however, that have helped me in the past and have displayed sensitivity toward the recipient. That's an approach that has worked for me in the past.
First of all, I approach the invite from a position of gratitude. "Thanks a lot for inviting me! I'm glad that we got to worship together". That sets the stage that you appreciated it and enjoyed your time together.
Then I express my desire in a way that is only reflective on me. "As much as I enjoy worshipping with you, this church isn't for me. I get more out of my current church." Then show that it's about your reaction to the church: "Do you want to come to mine next Sunday?" That shows your preference and that you want to worship together - just not at that particular institution.
If she asks why: I find that explanations for my preference never work out the way I intend so I stay away from them. "Why isn't my church for you?" "I'm sorry, it is just not for me. It's nothing that we'll fix and it doesn't change our relationship - I just find it's not for me." - and leave it at that.