Maybe a [-2] power for the first level, then [-1] for each subsequent level.
See breath weapon, incite emotion and variations thereof. For balance purposes, your at-will magic shouldn't cost any less than them for the same effect. And if it doesn't, why are you homebrewing instead of using existing mechanics?
Mythic Toughness against magic only with just one Refresh
When a spellcaster is putting pennies through your left eye with earth/air magic or icicles with variations of water/fire magic, your defenses against magic aren't going to help you. When a spellcaster is lobotomizing you with a pinpoint spirit attack, no amount of physical toughness is going to help.
going from spell tolerance 3 to spell tolerance 5 might actually be overpriced under that model.
Assume full caster at your EtA game level of refresh since we're talking +5 specializations;
[-3] Evocation
[-4] Soulfire
[-10] Refinement
Evo Specs: +1 control +2 tolerance for earth, +3 power +4 control +5 tolerance for spirit
Foci: +5 offensive spirit control, +5 offensive spirit power
Cost of "Tolerance" over his basic powerset: 2,5 refresh. Let's see what he can do with it;
1) Holy blasts that also degrade toughness at weapon 5, accuracy +15 at will, courtesy of Soulfire.
2) Lobotomies at weapon 5, accuracy +15 at will. Not quite instant mental evisceration but close.
3) Thrown objects at weapon 5, accuracy +15 at will. For when you need to ignore magic immunity and don't want to lobotomize people.
3) Always-on veils of strength 5. Perma-invisibility against anyone without superb senses is fun.
4) Arbitrarily high bonuses. He makes a sticky aspect at 5 shifts with spirit magic, then uses the "extend spell" option of evocation on it so it lasts until tagged at later scenes.
5) Make any skill replacements he can justify via spirit so his minimum roll for just about anything is +5
6) Summon lesser spirits at will. Never underestimate the capability of several dozen single-refresh Little Folk to kill stuff.
7) Conjure objects at will. This one is courtesy of Soulfire.
Hey, I'd totally pay 2,5 refresh over my caster's normal costs for the above. It beats getting Breath Weapon for 2 refresh who is going to give me a Weapon 2 accuracy +6 physical ranged attack
at best.