Although, there may be a longer more historical correct answer to this. I think it just goes more by what scales are used more in a particular style of music. Certain scales fit good with certain music, and some don't. You may see this if you learn more exotic scales, you may find that they may not work well with the type of music you wanna play. Unless you wanna be different, but in thoses days it wasn't easy to be different. The church was ten times more strict then, so anything they didn't agree with was forbidden.

Another thing, the locrian is different because of there root and the pattern that follows. This will give the scale a certain sound (tonality). Same with the lydian, it's the sound of the scale. They just probably thought it didn't sound good for church music. The sharped 4th and the flattened 5th are the same sound, but it's the relationship with the scale that gives it a different tonality. Like Relative minor and major, although they have the same notes, they're tonality is different.