Can a unit like Triarii be moded to throw javelins as Primary weapon while keeping spear as Secondary one? Or spear units (except Phalanx ones) can only have one weapon?
Have you tried already? If it doesn't work then there might be some things hardcoded, since spears and pikes are something special in the engine. If still you really like to have spears and javelins, then make the unit act like a swordsman, but model it with a spear and give it spear animations.