To get back to the antimatter. You could have very, VERY tiny little bits of antimatter enclosed in some sort of substance which doesn't interact with them (like maybe dark matter, and that enclosed in a regular matter shell) to make them safe to store and handle. Transistors, when first invented, were enclosed in big gobs of plastic so they could be seen and wired. You could rig up something which would pierce the enclosure when they needed to be used. A sort of grenade for a big finish.
Or just have the enemy swallow a pellet somehow, and let digestion do the work.
Or just have the enemy swallow a pellet somehow, and let digestion do the work.