Is it better to continue treatment with the non-Muslim female doctor, or to switch to the Muslim male doctor whose expertise is not unanimously agreed upon, given the previous issue of keratoconus?

If the Muslim doctor does not have sufficient experience, and there is no one other than the skilled female doctor to treat the patient, then there is no objection to being treated by her due to necessity. The patient must fear Allah, lower his gaze, and deal with the situation only to the extent of the necessity, for fear of temptation.