Killing a thousand Sith over years of warfare isn't that overwhelming. Especially not when, towards the end, the Academy sends it in all of its trainees and declares them Dark Lords, lol.
Quality > quantity. Traya beating down Atton with ease and B-teaming Brianna is better than Raskta carving her way through random Sith.
Not to mention that if we take the new retcon from the Revan novel seriously, Sion may well have cut down a thousand Jedi in his own right, and these Jedi are actually predominately experts in lightsaber and Force-related combat, not acolytes with unfinished training being hastily sent out to the battlefields to replace lost numbers.