I have not... my dog also hated to have her ears flushed out with a cleaning solution and then antiseptic ear drops... but since we had to do it twice a day she finally put up with it. Took two people though, one to hold her and another to apply the meds.
Try putting the meds on a tissue and then inserting the tissue down the ear (gently) with your little finger? Sometimes it is the tentative drip-drip that they do not like, but they don't mind a firm but gently touch.
You can ask the vet about oral vs topical, but keep in mind, if it is a yeast infection, then antibiotics may not be what you need. Also, I doubt that any oral treatment will not also need to be accompanied by cleaning out the ears.
If your dog shakes and scratches his head to get out the wax and discharge, and you do not help him, he may burst blood vessels in his ears and cause a haematoma... more complications.