It's not about damage per se. It's about messing with eezo and eezo based technology. Like Mass Relays. Also pure science.
And this statement is very misleading. Yes, the energies are comparable, but relativistic particles don't give out their energy all in one go. They are gradually decelerated as they penetrate deep into material. Moreover, dE/dX~1/E (don't remember the precise formula) or something close to that - the lower the energy of the bombarding particle, the faster it gives off energy (which is why most energy is released deep inside). The energy is given off in a multi-stage process. The outer layers of the target might even remain undamaged (or at least relatively so). With antimatter it's not so - the first collision will be the last one; all energy will be released at once (to at least it's more likely to be so); the damage will be concentrated. So, yeah, if you want to destroy armor, you need to either use antimatter, or low energy beams, and antimatter is far more efficient. High-energy (relativistic) particles will just go through armor. There are definitely uses for antimatter. Not to say about antieezo. Which, depending on how it reacts with non-eezo, might be able to freely pass through armor and only annihilate with eezo core inside the target.