The problem to me is that the Reals which aren't computable are absurd. We've never used any of them in all history. We can only put names on a very special few, those are countable, and we don't even know their value very well.
And the main way we prove that the Reals are uncountable is to use a proof by contradiction. It would take too long to spell it out, but they aren't really just contradicting "Reals are Countable". It's "All that other stuff we think is true AND Reals are Countable" that gets contradicted.
Once you accept the Reals, the Axiom of Choice is not simply obvious any more. And if you go down that path you get things like the Banach-Tarski paradox. To me THAT ought to be a proof by contradiction that we've made a mistake somewhere.
More interesting than that though: If the universe we live in requires non-computable Reals to describe it carefully, then it says something very weird about determinism. In order to compute a future state of a system, we need to use numbers we can't compute?!?