I think a fixed penalty to strength (-6) is a decent fix to prevent a maximized ray of enfeeblement (-11 strength) from being one of the better opening salvos in the mid to high level wizard's arsenal.
Considering that for the average two-handed weapon fighter each of his attacks would be facing a -3 to hit and a -4 to damage this seems to be a pretty significant penalty which continues to remain a viable tactic later on into the game versus the average 1st level spell's increasing uselessness.
The other option would be to add a fort (negate) save onto the spell which would prevent high level fighters from being utterly gimped by the spell.
Considering that for the average two-handed weapon fighter each of his attacks would be facing a -3 to hit and a -4 to damage this seems to be a pretty significant penalty which continues to remain a viable tactic later on into the game versus the average 1st level spell's increasing uselessness.
The other option would be to add a fort (negate) save onto the spell which would prevent high level fighters from being utterly gimped by the spell.