After being one who always automatically eliminated Byg's supply in my game, I have come to accept it, if only because it seems to have become standard in all newer versions of SS and picking it out each time is a hassle. Also, I do some modding myself and if I present a submod to the forum I have to reinsert Byg because many people ask for it. You get used to it, and it does have some interesting aspects.
One way to do sieges is by having two generals working in relays. When one of the generals is out of supply, with troops weary etc. swap him with the other fresh one. Voilá! The whole army is fresh and resupplied. Because you see, is it not the army that is unsupplied, it is only the general...

And not necessarily consider this an exploit, you can view it as a reinforcement bringing in supplies, replacements and a new perspective to the battlefield.
I think the rationale behind this submod (and others like Pnut's disease system, which is also present in SS) is to make you assault cities instead of sieging them out. Like, they want to force you to "have fun"... their way. I don't think this is nice, each has his way of skinning a cat, and long sieges was one historical way of conquering cities. Besides, in the early game before you get catapults and trebuchets, it is practically the only option because assaulting walls with peasants and spear militia isn't very conducive to victory.