you are correct - mods can be changed during the game. Simply edit the mod file, save the changes, and reload the mod (that is, go to mod preferences and turn the mod off and then on again)
One possible issue with this sort of change is that the AI can uses those spells fairly well as long as it isn't human controlled
In my current game, pangaea is making excellent use of centaurs with gift of madness. I haven't really had much problem with breath of winter, but it's not that great in Dom3 - fatigue is a nuisance, but its not fatal like it was before.
Also, its possible that gurus with gems for enslave mind or some such will now waste them on blink, making a bad problem worse, but I doubt it. It does make blink spamming hard, not that it was that useful anyway.