I honestly don't agree with this idea. Guilds like Alumni would clearly have an advantage over every other guild and it kind of ruins the purpose of most towering tactics, such as rushing flag, surrounding flag, defending stairs, defending halls, setting a sub tag to defend in halls, etc. I don't see how this idea at all helps towering. The way I see it, it's basically just promoting guild spar, which isn't a bad idea, but I think you're taking it too far with the whole "having the beat the holding guild to take it." I agree with Craftz: it would pretty much destroy towering because you're taking away so much from towering by adding a guild spar. Towering mainly focuses on attacking the flag or defending the flag, and both of these would be taken away.
Not a lot of people like to guild spar. Some people prefer towering over guild spar. What happens if you completely turn the towering system into a guild spar system? Many people who enjoy towering would probably leave. There would probably also be those seven-eight dominating guilds that will always be hogging a tower (*cough* alumni *cough*) and they probably won't want to recruit anyone who doesn't have a positive spar score.
Almost everyone has experienced some form of towering. It's the second stage in your Graal life, you could say. When you're still a noob, you see towering and your want to get involved and try it out. If towering is forcing you to guild spar, then noobs who are curious about towering probably won't even get to tryout since nobody will recruit them, and if they do happen to get recruited to some kind of noob guild, they're probably be defeated by the current holding guild.
This system is basically just a massive upgrade for sparrers and a very big downfall for current towerers and the current towering system. Hopefully you see why this isn't that great of idea. Guild spar should get more attention, I agree, but not like this.