I see your point John. One way or the other though, heroes are going to be able to gain access to spells so long as the Sovereign imbues them with essence, this has been known for awhile now.
The only difference between what we currently know and the proposal here is that currently heroes may have access to every spell (Saying may because I don't know how combat spells will work), this proposal would limit them to a smaller selection.
The scenario you described, and I agree is deeply troubling... Could be used either way, and fixing such cheap tactical exploitations should be tackled with certainty, but I don't see how the proposal here in anyway adds to the problems of such tactical exploitations. If anything it is one of several additional steps that need to be taken to address such.
Using your own example, would the three heroes you mentioned be any less imposing if they had access to every spell that you've researched? Perhaps such possible spell related tactical exploitations is why Frogboy proposed a Winner takes all approach in the first place. To prevent cheap skirmishing tactics using A-bomb lobbing heroes.
Another possibility would be when separating certain magical potential in heroes, allow only the most powerful spells to be used by "Genius" level heroes.
We still face a Finite amount of SoV Essence as a balancing factor, combined with the max allowable Mana any one Hero can generate to control how many spells can be used, or how many and what level of magic one possesses.
The "Buy" the Magic Books idea seems very doable. Perhaps the method of Learning spell for Hero's is to use their Mana initially, such that they will require some re-gen time to be able to actually cast those spells? That would be a great check and balance to a Embue - Buy Book - Start nuking Now, sequence when otherwise you should have had to simply run away prep, wait and then start the nuking process.
I guess what I fear, and it is a Balance issue many times, is that The Magic part will quickly outstrip the War (army) part of the game play. Invariably, and I have sen it before, is that the almighty powerful tools have a way of making the rest of the process moot and every game turns into a race to the end power game.
There is absolutely no reason to waste valuable Resources or precious Turns on building a army that has a lifespan of 38.5 seconds, come 275(?) turns into any game when Fire Magic has been, and can be, rushed to.