only a symptom of a deeper problem, namely that the \mathcode, \mathchardef, \delcode, \radical etc. primitives are deprecated with LuaTeX since they (unlike \char etc.) can't easily be extended to allow Unicode code points. Therefore all packages that make use of any of these primitives need to be fixed. I can't imagine that rewriting the world is either feasible or desirable. Presumably "deprecated" means "if you want new functionality use new primitives, existing primitives will keep working as they always have".