These super guilds already exist now, literally the only difference in my idea is that their sub members would not damage the flag. Now, as Goat said, this would allow 20 sub members to crowd around flag and have very limited (4) people healing flag. I don't understand how this is bad and I dont see this happening. Is it any different from having 20 members crowd around flag and having 4 members block/pk attackers? It's not.
In fact since allies do not respawn in closer areas than the actual holding guild, it seems like this really wouldn't help hold the tower at all. And even if it did, if you have that many members YOU SHOULD be able to hold the tower without any problem.
This is like NO different than the system already is, the only times that people on sub-tags/allied-tags effect the outcome is if they are either trolling and trying to abuse their tag or a noob who doesn't know what he/she is doing.
This would just eliminate these problems, while not affecting the gameplay in other ways.