While I support new guild for the game, I dislike the minor guilds for a lot of reasons listed before. But it really boils down to one thing for me: Depth vs Width.
I like SF's plan to introduce more width to the game by adding more guilds than just keep adding to existing ones, but I feel the Minor guilds are the wrong way to do it.
The major guilds could stand for just a little more depth, in the form of a third captain and mascot for each of them. Those key models open up a lot more replayability in each guild, rather than the current binary available. Adding a third Captain refreshes the potential of playability for existing models, instead of just adding more "Squaddies" to the roster to fight for the same 4 spots.
Minor guilds offer some new options, but as stand alone guilds, they have less overall depth than the core Guilds, so while they add some temporary interest, they have less long term interest potential, so people will likely be quick to discard them in favor of something that can keep them coming back for more.
Of course, the minor guilds does encourage people to get the corresponding major guild as well, which is likely part of SF's overall plan to "sell more stuff".
So while I don't think Minor Guilds will kill off Guild Ball, I don't think they'll do the game any favors in the long run.