I think it was, yeah. I don't think it was the injury itself, though that was certainly horrific, but how Slade treated Bart, the utter disregard and disrespect. Bart's supposed to be one of the Flashes, someone who runs through time and other dimensions, who fights the biggest, wildest threats in the multiverse....and a dude who's marginally stronger than normal considered him a joke barely worth acknowledging.
I think Slade made Bart realize that everyone saw him as a screw up, Slade taking him down so easily likely made Bart think the same, and I think that's what hurt more than the kneecap.
Inertia and the Rogues killed him, but that actually shows a degree of worry and concern; Bart was dangerous enough to kill.
Plus, the villains here and the relevant stories all came from around the same era, which did mark a shift not only in how YJ was treated but the DCU as a whole. When Johns put YJ into the Titans it really was the beginning of the end for these kids, even though Johns' run itself was popular at the time and sold well.
Plus.....almost nobody remembers who the hell Inertia even is, and that likely played a role too.