It sounds like you need an 'In-between' Blendshape so it doesnt intersect the eyeball. Had the same problem myself recently.
Just dupe the object when it intersects the eye, pull out those cv's or vtx's, and open the Options for Edit-Add-Blendshape. Click 'Add In-Between Target'. The Target index refers to what existing Blendshape Shape you want to add this too, and the In-Between Weight is when you want that InBetween to happen.
So, when you've added it you have a Open eye at say 0.0, an inbetween Shape at 0.5, and a fully closed eye at 1.0. All controlled through one BlendShape slider.
Neat!
Thats been in there for ages and I never knew about it.
good luck!
seanman