"HW rulez" mod (add-on) for HoMM3.

I don't think it's so much about the starting Tower, as I understand it. Players always try to build a Guildhall in the Tower (in their town or a captured computer town) using the Library. Rebuilding the Library in addition to rebuilding the Guildhall itself gives too much of an advantage, which is what many strong players don't like.

Actually, no, disabling the Library upgrade prevents it from being upgraded, even in your own Tower. As for the appearance of a nearby neutral (computer) Tower, that's an acceptable random event, and there's no more imbalance here than there is with getting Control from the very first Utopia.
And even with the Library, Control doesn't always come quickly. Sometimes, Town Portal is only available after the 4th building, and Double Damage only after the 3rd.