It has often been said that a duke CAN be killed with proper RP, execution and luck. However, in practice I'm pretty sure any DM(s) would make the execution and luck part IMPOSSIBLE, simply because of the repercussions of what would need to be done to move forward from such a change. Is that necessarily a bad thing? In PnP if a character tries to take the story too far off the rails the DM either has to decide to scrap a TON of work and go off the cuff, do something to force them closer to one of any number of rails they've planned for, or cause the PC to fail. Is what occurs in BGtSCC so different? Especially when you consider a PnP group of 3-8 players+ a DM vs. BG having dozens of players and multiple DMs, I think a bit of 'glass ceiling' should be acceptable to support the sanity of staff and players not involved in whatever earth shattering/lore breaking event might take place.
I got no skin in the game here and this is woefully off topic which is supposed to be about Guild Leadership by retired players, but on the tangent of NPCs, in a game where the PCs could smoke Elminster (or whoever) that would likely only occur at the very end of a game before that party is retired and the group moves on to some other game (D&D or otherwise). On a persistent server that isn't really an option, since the whole of the server must move forward after whatever occurs.
In general, I think guild leadership of the "Lore" guilds is exactly as it should be. The Red Wizards are a satellite trade guild of Thay, their is a PC leader, but he/she does report to higher ups that are offscreen for the most part since they are in Thay. The Thieves Guild is not a part of the Shadow Thieves and thus it makes sense that the Duchess (or is it a Duke right now?) of Shadow is the highest ranking leader, but how much power does the Thieves Guild really have anyway? I suppose the DMs could install Alatos "Ravenscar" Thuibuld, but there is no need... He is not necessarily the leader of the Thieves Guild in our (1e) timeline afterall. So in general I think the guilds are fine as they are, but certainly if there is a disagreement than the HDMs and Admins should be notified and all parties should attempt to come to some kind of agreement as to how everyone can come to some mutually acceptable path forward.
Frankly, I don't have the time to dedicate to getting in game, but if I did I would want to spend it playing. This is why I said previously, and still believe the best approach is - just switching to a guild that won't require so much OOC/out of game effort. But to each their own.