'I feel this side of the Christian tradition deserves examination, as it is the unquestioned assumption that Christianity is a "good" philosophy and it is only its malpractice which is "bad".'

Unquestioned? I don't think so.

For sympathetic views of Judas, see a wonderful story by Jorge Luis Borges called in translation, if memory serves, "A German Requiem". Though I think it was originally a Gnostic "heresy". And of course Jesus Christ Superstar, which comes down heavy on Jesus's side but still has some sympathy for Judas.