Here's the music theory behind what you are trying to do.
The traditional hymnal arrangement of "Holy, Holy, Holy" can be played on piano or organ, but it is really a chorale arrangement. It is choir music, designed to be sung in four parts: soprano, alto, tenor and bass. When a pianist plays it, she is actually just playing the notes from the four vocal parts.
Mosts hymns are traditionally arranged as homophonic chorales. The four separate vocal lines add up to a different chord for every single melody note in the piece (or, at least, quite a lot of chords presented in different inversions). The inversions (the "slash" bass notes, like "C/G") happen because there is a bass line in the arrangement.
It is possible to completely transcribe a chorale hymn arrangement for guitar and to preserve most of the four voices. It's the sort of thing that a classical guitarist would do. The best arrangement you could come up with would try to preserve the melody line (soprano) and the bass line, playing both at the same time on your guitar, and filling in the alto and tenor harmonies in the middle according to whatever could be reached on the guitar fretboard. This would be a very difficult task, however, and something that only an advanced guitarist would undertake.
For your purposes, you need to make up an accompaniment that does not involve homophonic chorale voicing, because that's much too complicated for "contemporary" worship with a guitar. All you need to do is find chords you can strum that can accompany the melody. Don't worry too much about inversions or a bass line. Root-position chords will work okay. Just find about one chord per measure that you can strum while someone sings the melody. If you want it to sound really good, find a bass guitar player who will play the exact bass line from the chorale hymn while you strum.
For your enjoyment, here is Christopher Parkening playing a solo guitar transcription of the traditional chorale arrangement of a famous hymn. In the first verse he plays the chorale, similar to what you'd see in a hymnal (listen for the distinct bass line he is playing), and then with the second verse he varies things a bit in the upper voices over a pedal-point (drone) bass.
