Music needs to breathe, and must be phrased intelligently. Unremitting legato, where there are no breaks in the sound, is rather like speaking without any breaks for breathe Which is necessary for the listener to understand the words being spoken. Unremitting legato playing can be very boring for the listener, it can make it hard to understand the music. An unremitting legato style is probably why some people not enjoying listening to organ music.
I would suggest thinking how you are going to phrase of the music and then work out the fingering once you know where the breaks in the phrasing are to occur. Work on the fingering after you've worked on the phrasing. In some scores, where there are no phrasing marks, you can look for the natural breaks in parts (which often can be found where there are big changes in position of the notes) to find the end/start of phrases. Think about singing the score, where would a singer take a break?
Legato playing is an important skill and many of the organ tutors have sections on developing a legato style of playing: the old Stainer Organ Primer has pages of exercise including chordal substitution exercises. For hymn playing a legato style is important, but again this needs to be phrased to reflect the text of the hymn being accompanied.
Iain