Obviously non-context-free grammars are a problem, but a GLR or PEG grammar is still perfectly refactorable.
You forget that refactoring an intuitive grammar to LALR involves totally mangling that grammar and making it more difficult for everyone.
If the language is expressed as a GLR or PEG grammar then tool makers have it easier I reckon - easier to understand grammar.
The way to really ensure it's easy for everyone is for the compiler write to provide some abstract yet intuitive representation of the underlying grammar.
It really isn't an either/or, it's a case of both at once, I think!