That's all a matter of taste really. Personally, I happen to think that in spite of its splendid visuals and a few outstanding set-pieces, THE CHURCH is a thoroughly rotten film that just isn't worth wasting 90 minutes of your life on. I'd put it on the list of my bottom 10 of euro horror films. Yes, really!
THE SECT on the other hand is a film much more to my liking. I liked the story and the characters, and it kept me very much entertained and impressed with some excellent visual touches and effects.
But that's me - I know there are plenty of others who will tell you that THE CHURCH is the superior film. In any case, I think both films suffer a bit from the involvement of producer Dario Argento because it's obvious that Argento and Soavi want different things. It was only after he was free of Argento's influence that Soavi was able to make his masterpiece, the outstanding DELLAMORTE DELLAMORE.