Write in Fingering
If you have difficulties with your hymn playing, I highly recommend that you pencil the best fingering in your hymn score. I think this is important because if you know the exact fingering in any given place, you are more likely to avoid using accidental fingerings. Accidental fingerings might just be the reason why achieving legato is difficult for you. So work out your fingerings in each and every measure, at least until you have more experience. Once you know the best fingerings, stick to them in your practice.
Use Finger Substitution
Finger substitution is a technique which helps achieving legato on the organ. By using this technique, you play one key with one of your fingers and then change to another finger while holding the same key. This technique works for holding two or more notes in the same hand as well. This is called double or triple substitution which is used in more advanced chromatic organ music.
Use Finger Glissando
Finger glissando is a technique in which you slide from one key to another with the same finger. You can employ finger glissando from the sharp to the natural key (the most common and easiest), from natural to natural, or from natural to the sharp key (the most difficult). The thumb glissando is the most often used. However, take care not to use this technique too often. As finger glissando is rather awkward for the beginner organist, in most of the instances you can solve the legato problem with finger substitution.
Use Finger Crossing
The least common legato technique in hymn playing, finger crossing might be achieved by putting a longer finger over the shorter one. In contrast, the shorter finger might be placed under the longer finger. Most often this technique is used in large chords and octaves which are absent in hymn playing.
Treat Your Hymns Like Organ Compositions
Although hymns are deceptively simple and short, the best way of practicing them is the same as in real organ music (at least for the beginner). Practice your hymns in shorter fragments, maybe one phrase at a time. If you have trouble achieving legato, play each of the voices separately. Try to play the phrase at least three times in a row correctly. Then practice playing various two voice and three voice combinations. Make sure your fingering is precise. Only after you are fluent in three voice combinations play all parts together.
For most people, the right hand technique is more developed than the left hand. Therefore I recommend that you take the soprano and alto voices in the right hand and the tenor in the left hand. Take advantage of the pedals in the bass part. Although there may be many options in distribution of parts between the hands and feet, this is the most common disposition in hymn playing. If you can play an interval of an octave with one hand, follow my suggestions and you should have no problems achieving legato in hymn playing.
If you would like to know more about hymn playing, I highly recommend studying Organ Technique: Modern and Early by George Ritchie and George Stauffer. This method book has separate chapter on hymn playing with many important exercises.
Another great resource is Art of Hymn Playing by Charles E. Callahan. It has 250 Introductions, Preludes, Free Accompaniments, and Alternate Harmonizations. The pieces range from 2 part voicing to more complex. It is meant as a graded guide to hymn playing.
By the way, do you want to learn to play the King of Instruments - the pipe organ? If so, download my FREE video guide: "How to Master Any Organ Composition" in which I will show you my EXACT steps, techniques, and methods that I use to practice, learn and master any piece of organ music.