I proposed a solution not too long ago that would completely solve the entire "mass-recruiting random people to help defend tower" thing, and thus make this bug moot.
When a new player is recruited to a guild, there is a 10 minute period in which the player is still fully a part of the guild, but cannot help defend a tower if said guild is already in control of said tower. Meaning, as far as the game's mechanics for towers are concerned, that player would not be considered a part of the guild. If 10 minutes go by and the guild is still in control of said tower, that player may now help defend.
All problems solved.