I have successfully repaired much worse holes than that. Sure, you'll have to replace eventually, but if the waders are otherwise solid, that looks very repairable imo.
The basic method you describe for repair (roughening, cleaning) sounds good. I never had good luck with Shoe-Goo on waders. It does not seem to bond well or hold up over time. Much better results with Aquaseal. A patch of material over that spot on the boot may also help strengthen the repair.