Sure they could've. Johns took away Barry Allen's parents without a full on reboot. He just used time travel. The Super-titles could have done the same thing. The Kents died because of a 5th dimensional battle that took place across Clark's entire life; it'd have been pretty simple to retcon the Kents out of the mythos.
Of course, people would have been up in arms over it worse than they were about Nora Allen being murdered. But it *could* have been done, and likely wouldnt have caused much more complaining than the full reboot did.
I think the hardest thing to get rid of would have been the marriage. Even with 5th dimensional hijinks at play, people werent likely to let go of that without a fight.