Igrik, here is my idea. I worked a bit on, so if you like, you can develop, if not, I will only use for local because I love your mod but want total control on level up.
I changed mod name so it does not interfere with original. What I did:
1) Added full control over primary skills, so now you develop your hero 100% your wish.
2) I don't know how to work with the hook, so I manually remove the primary skill he gets before script
3) Did not scripted the OK button to be enabled only when player selects both bonuses yet, waited to know your opinion first.