I was on Highway 10, passing through a small town. I stopped on the side of the road, due to a sharp pain from my kidney stone: I put my emergency flashers on.

My daughter had to use the washroom, so went inside the Tim Hortons that was beside us.

in the meantime, after about 1-2 minutes, I noticed a Police vehicle pull up behind me...I turned off my flashers and proceeded into the parking lot. The officer followed me, got out of his vehicle, and asked for my license/insurance: when I inquired why, he told me I was stopped on a sighed highway: I mentioned to him about my sharp pain, and that I was there only 1-2 minutes.

In the meantime, my daughter returned to the car, and he asked her for her name and address (why?)

He was in his vehicle for about 10-15 minutes: he then came out, told us to wait, and proceeded into Tim Hortons, where he inquired all the staff about how long my vehicle was stopped outside...

a total ordeal of about 40 minutes, after which he gave me this ticket

He said I can come back to fight it, with medical proof (which will cost me more in time and gas to come all the way out there)

Was this a bit excessive? Do I have a defence?

I feel that his time could have been better spent than this

It sounds like he charged you under subsection (12), interfering with traffic. If you can show that you had pulled sufficiently off the road that you weren't interfering, you could have a case.

I have no idea why he'd have asked your daughter for her name and address. It was also interesting that he'd have questioned the staff at Tim's as to how long you'd been there unless he was willing to cut you some slack on the exemption for temporarily being there for emergency purposes.

If I were the officer, I'd have probably let you go. After all, you did move off the highway and into the parking lot. If I were you, I'd fight it. But not everyone wants to invest the gas and travel time needed. There are no demerit points for this offence and it would count as a minor conviction for insurance purposes.