Have had the same issue, and did the same mistake with my own mods. Ive rectified a lot, and the game became much more fun for me. Ive added my notes in the WIKI, along with the statchanges that comes with traits, so people can avoid making 100/100 girls. If one of you fine gentlement would note a bit more on the wikisite, that might be a good idea - you drive compelling arguments.
I really like fires_flairs idea of girls "levelling up". So if a girl has a max stat of 100, it doesnt matter, since at lelv 0 she can only go to max say 45. Then 55 at level 2, and so on. Then if the girl had a stat at 48, she would stay there even if she goes to level 3.
But I also think this might break the game, as youd need girls to level faster - which would mean they bring in more money, again giving balance issues.
Maybe put in something simple, like that no girl can have a statline over 55 unless the Matron has a higher score ?