spore clouds have a special attack that creates a fungal tile in their space at the cost of their life. It should be pretty easy to modify it’s chance to fire or remove it all together. I haven’t tested it, but have considered the issue before. I don’t think this will stop spread entirely, but it should be able to slow it down significantly. Of course, aged spore clouds evolve into fungaloids eventually and the clouds are spawned in huge numbers…so you might just be trading one problem for another plus lag.
edit: Check out the Fungus Fighters Kit. It doesn’t affect spread rates, but it gives you more effective tools to fight back. I have no idea if it works with the current version, it’s fairly old.