I think the simple solution is to make creatures that were designed to be immune to something should always be immune even if magic comes into play.
I'm a skeleton! I'm undead! You can't critical me, hello, I'm UNDEAD.
*graveseal*
Awww, crap, I'm less undead now and vulnerable to crotch shots again with graveseal!
Or maybe graveseal is a weakening the bond between the animated feature of the dead and makes the bones more brittle and weakens the spirit bond of the person. Who knows exactly how the magic affects the individual to which it is casted. We also do not know exactly the reasoning behind the immunity of critical hits. It could be they have no squishy parts, or it could be that they are magically enhanced spiritual bonds prevent the weakspots from being exploited.
One could mod in the nerf into the game currently. It would take some time, as there are a few ways to do it.
One could force the immune to crit to automatically cast a spell at the beginning of combat, to which graveseal cannot stack with (not sure if that would work, but it is worth a try)
Determine the creature type and force the spell to last the duration of 1 if the creature is a skeleton -1 otherwise.
Or the simplest nerf of all make the spell last 3 turns.