Write in Fingering
Very often people do not play with a good legato because they do not know the best fingering. Because it is harder to use the proper fingering if it is not written in the score, I suggest that you write in your fingering. It is especially important that places which are the most difficult in achieving legato would be fully fingered. Do not hesitate to change the fingering if you find a better solution. However, erase the old markings and write in the new ones as you practice for best results. The same applies for the pedal part, of course.
Finger substitution is generally accepted as the most common means to achieve a perfect legato on the organ. However, it should be used wisely. For example, most often there is no need to apply finger substitution in a one voice passage because the legato can be achieved by using position, scale and arpeggio fingering in such a case. However, for episodes which require playing more than one voice in one hand, you can use finger substitution technique. Basically how it works is like this. While holding the same key with one finger, you substitute it with another finger. In chromatic music, this technique can work on chords where you substitute more than one finger at a time (double or even triple substitution).
If finger substitution cannot be achieved and all your fingers are busy, another option would be to use finger glissando. With this technique, you slide from one key to another using only one finger. In some cases, double glissando is also a possibility (sliding from two sharp keys to two natural keys). However, make sure that there is no other way to achieve the legato besides glissando. Quite often you can take the burden of one hand by playing a few notes with another hand. Whatever you choose, always write in your solution in the score.
Like finger glissando, finger crossing is not a very popular technique but sometimes it is necessary to use it. In finger crossing, you place the longer finger over the shorter one and vice versa. This technique is useful in playing wider intervals, like sixths, sevenths, and octaves legato. Usually finger crossing works best with fingers 3, 4, and 5.
If you take my advice, write in fingering and use finger substitution, glissando, or crossing in your choral accompaniments, you can achieve a perfect legato even with small hands. More often than not the legato playing depends not on the size of the hands but on the choice of the fingering.
The practical techniques of accompanying the choir with or without a conductor are discussed in Organ Technique: Modern and Early by George Ritchie and George Stauffer which I highly recommend.
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.