Of course it's Dia dhuit answered by Dia 's Muire dhuit (and sometimes Pádraic added on in good measure) but the question I have is this - how would an Irish-speaking Protestant say hello ? I'm not at all sure that they would want to say the same thing.

You can answer with "Dia dhuit" too if you want to. I'd imagine that would be ok for anybody that believe in a god.
I'm an atheist and I use the traditional greetings.

Ceart go leor. I've heard that there are some people who get round it by asking straight off - Conas atann tú ? (or the other equivalents) and then there's - haigh - is that used much?

You could if you wanted to start a greeting with: How are you? Conas a tann tú? Munster, Cé chaoi a bhfuil tú? Conamara, Caide/Goide mar atá tú? Ulster. Or the haigh, haló, or hiya too. Regardless of religion. And less formal.
I'd likely say Dia dhuit to an old person. Haló to others. And haigha to somebody I know well.

Personally I hate when people ask "how are you?" in any language. When they have no interest whatsoever in your health.