If you want to include a word or phrase in Greek in a novel, should you write it in Greek letters or should you transcribe it by pronunciation?

A novel with mass readership, not in Greek, where you don’t want to alienate readers unnecessarily, and you care to give readers some notion of what it sounds like? Use transliteration rather than original script. Same as if you were putting Hindi (or whatever your language happens to be) into a non-Hindi (or whatever) novel.

Yes, I write Greek in Greek characters here, and when I don’t, I use IPA. But I’m not writing a novel.