[Endoperez]

You can also use your magic. Elephants have poor magic resistance AND poor morale.

Alteration 3 gives Body Ethereal. Area of Effect 1 means that 3 human-sized units, per casting, become ethereal and ignore 75% of all nonmagical attacks, including trample. With 4-5 S1 mages, that can be few dozen legionnaires.
S2 mages and Thaum 3 or 4 can be used to spam Paralyze, which will quickly stop the elephants.
Alternatively, you could go for Evocation and cast Shadow Bolt. It deals damage, paralyzes, and even if you miss it won't affect undead.
Any fear spells, including the lowly Frighten, can be used to great effect. I think Frighten is in Thaumaturgy, but I'm not quite sure. Just look for Death 1 combat spells in the manual if you can't find it.

Also, every elephants costs over 100 gp. Your undead will be very cheap compared to that. Have lots of undead waiting for the elephants, and cast spells and fire javelins at the undead; you won't mind having few less undead, but killing the elephants will really hurt your opponent.

Also, if the elephants' commanders don't have bodyguards, use groups of Longdead Horsemen to kill the commanders.