Well..not really taking advantage of game mechanics, and I hate how everything is labeled as that.
Guild Masters View: He can delete most, it's his guild. whatever he says, goes.
Second in charge: The deletion of many members is easily roleplayable. Here's one senario I can think of, the second holds council with the guild master and tells him that a few low ranks are planning to impeach him. He ask for permission to remove these traitors, and so removes all the good guys, and leaves baddies, (This is if the second is bright, and the guild master is an idiot.)
Also, mass murder, expulsion, it's all happened before. So, deleting a majority can be done in an RP way, and doesn't really abuse game mechanics...If you're overthrowing a guild, why care about the rules of deleting people? It's do it all the way or die at that point.