The "epic takedown" as you call it was tongue in cheek. Neil and the boys in Skynyrd were friends. Ronnie Van Zant often wore Neil Young t- shirts on stage and wore one on the "Street Survivors" album cover.
It all began with 1970’s ‘Southern Man,’ which — like 1972’s ‘
Alabama‘ — found Young boldly confronted the history of slavery and Jim Crow in the American South. The idea of lumping in all of the region’s modern-day denizens with those misdeeds sparked ‘Sweet Home Alabama’ in 1974. “We thought Neil was shooting all the ducks in order to kill one or two,” Skynyrd singer Ronnie Van Zant
later said. “We’re Southern rebels but, more than that, we know the difference between right and wrong.”
You're correct in that they both had respect for each other however Sweet home Alabama was clearly a takedown of Neil Young.