Welp, SBY ships have positron weapons as main guns, but they also have missiles and torpedoes. Though beams of antimatter might be something the Replicators can't quite adapt to.

And, if the Andromeda Class can also use kinetic shells like the Yamato, which can interchange (it's never been demonstrated on screen, but they're based on the same technology), then Avalon could give the Replicators some hurt through the old fashioned Tau'ri way.