I don't think the problem is that the military guilds exist. I think the problem is that they've become one of the only types of popular organized guilds that spread out over the map. Throughout the years, there have been pk, spar, guild spar, social, tower, school, and then some more abstract ones like for playing since X, or having Y amount of whatever stat. No matter what, these guilds were always out and about doing stuff.

The pk, spar, social, and tower guilds still exist, but they now are only found in the Battle Arena, at a tower, or idling somewhere and only socializing through guild chat.
In other words, take you and your guild anywhere other than an idle spot and communicate through overworld chat.