I agree that raising the guild level guilds have to reach to become eligible for GvG will spare new guilds from getting hit, but it depends if that becomes counterproductive in terms of losing potential GvG targets. I'll leave that to the GvG afficionados to debate.
I think a large part of the problem with fledgeling guilds having a hard time, starting, flaming out and dying would be solved by increasing the minimum level the founder has to be before he is allowed to start a guild
Too many young guilds are doomed to fail because a new player enthusiastically starts a guild before he or she fully appreciates the game, and lacks the personal experience and in game resources to made a good go of keeping a guild alive.
Starting a guild, and then discovering it is much harder than it looks is tough - it could then be that gvg happening is the straw that breaks the new guild's back as it were, and causes the members (and founders) to give up the ghost. Or not, I'm sure many new guilds fold because it is just hard to get and keep enough players, especially new players, who nowadays can get into well established guilds without much difficulty.
But I do think that you are allowed to be a guild founder at too low a level, and this can lead to avoidable failures, and loses not only that new guild, but possibly the founding player who may quit the game in frustration after sinking resources into a guild that needs a lot of luck and persistance to fly.