The simpler suggestion of increasing their resource cost (to represent the difficult task of catching/breeding and then training an elephant, not to mention the expense of feeding it while you are training it, and the expense of a proper howdah and harness) would also make it more difficult to mass huge hordes of elephants. But alone, it doesn't address the "elephant plus hoplites" problem.
As a quick fix I favor higher rescost, but ultimately I'd like to see parts of squads allowed to rout while their braver squadmates fight on. Even if I have to wait for Dom4 to see it.
