Here's what I'd do. The Psionic version (Incarnate) can't be dispelled with a Dispel Magic/Negate Psionics. It can be taken down with a 9th-level power (Psychic Chirurgy, I think), OR, by using Incarnate again.
So, let's change both of them. Make Permanency/Incarnate act like this:
> When dispelled with the usual (Dispel Maigc / Greater Dispelling / Negate Psionics), the ability is only temporarily suppressed (as a magic item). The usual caster level check is needed, but there's no minimum level.
> They can be negated by casting Permanency/Incarnate (either one) on the person (no XP cost? It's just a special use of the spell, sorta like countering). But in this case you make a caster level check to see if it worked, and you can only do that if you are of higher level than the original enchanter was.
> Or, they can be permanently negated with certain high-level spells (Wish / Miracle / Psychic Chirurgy) automatically. You cast it, the Permanency is gone.
Maybe there should be an XP cost for the removal. Maybe tweak the ranges.