If I'm understanding correctly, you have an IK chain with bones that you want to scale, but the IK constraint is preventing you from altering bone scale in the way you want to?
Not sure if this quite solves your problem, but I've just tested a workaround that might help. For an IK chain with bones named A and B...
1) Create a bone that is a child of A (and a sibling of B). This will be your scale control bone. (It can't be a child of B)
2) Create a transform constraint from B to your control bone, and set it to match the scale.
3) You can now alter the scale of B by changing the control bone.
NOTE: When I was mucking around with it I found the scale constraint MUST be ordered after the IK constraint if it's going to work in FK mode; if reversed, then scaling will affect the IK mode but not FK. Creating a version of the constraint both before and after gave both behaviours.