Considering all the crap I've seen slipped into appropriations bills in conference commitees, I think you underestimate the potential for mischief. Don't assume that the union hasn't long prepared such targeted legislation in order to slip it through in the noise over the budget.
The session ends today. The Governor can, and probably will, call the Legislature back into Special Session to deal with the budget. The nature of Special Sessions is that the legislation that is introduced in the session must deal with the purpose of the session, i.e., the budget.
The only thing that can be slipped into a budget bill is control language for spending items in a budget bill. Some control language even has to be passed by means of a separate "trailer bill." The rules of drafting and placing amendments in bills are that amendments have to be germane to the bill's subject. The Legislature does not act like Congress, which can place any amendment on any topic into any bill. Happily, the California Legislature doesn't operate like Congress in this regard.
While I share the concern about protecting homeschooling, considering the rules of germaneness, and the rules governing special sessions, I doubt a bill as explosive as one that hems-in homeschooling would or could even be introduced in a special session. I'm not speaking wishful thinking, but from over 20 years experience working both in and with the California Legislature.