(Envisioning Lo Pan and Egg Shin's spell battle at the moment, thanks to this thread).
Once a caster starts Spell Of Making, really the only way to stop it that I can see right now is taking out/attacking the Sovereign casting it. Of course, you could add the requirement that you retain control of the four towers during casting, or else the spell gets disrupted.
Another thought would be to have a 'counter spell' to Spell of Making, where you could sap Mana from the caster attempting this (thus increasing his casting cost). This would have to be a steep ratio - I'm thinking 4-5 mana per mana sapped from Spell of Making, or higher based on the total number of opponents - otherwise it would be too easy to disrupt. I'm thinking that you would have to have a significant lead in Mana to attempt a Spell Of Making victory with the counter ability in play.
Or, a variant of this would be to increase the cost of the Spell Of Making based on the number of shards NOT under your control. So, say you controlled half of the shards, the cost would be 500, but if you only controlled 25%, the cost might be 1000 or 1500... This would strongly encourage a player to take over enemy shards, assuming the mana cost was more appropriate.
The base cost for Spell of Making should be based on the total amount of mana (per turn) available on the map. I usually play with abundant magic, so the shard frequency should affect the spell cost. I'd suggest scaling The Spell Of Making mana cost to the total number of shards on the map: less shards = lower cost, more shards = higher cost.
The 250 cost in my last E:LH game seemed quite low. For some reason I was thinking it was 500, but then I remembered that was for that plague event I've seen a few times now. Also, we've had the 'moving it down the tech tree a bit' discussion in another thread already.
Your idea is definitely interesting, and I like the tie in with the Legendary concept.