Interesting.
Inverness-shire is a very large county, and it's about 110 miles by road now from Oban to Inverness. Even Fort William to Inverness is 65 miles.
In the 1860s it would have been much further by road from Oban, because the road had to go all the way round Loch Creran and Loch Leven. It also required at least one ferry crossing, at Connel, and there was another at Ballachulish which would have avoided the long trek round Loch Leven.
It would have been possible to go by boat on the Caledonian Canal, and possibly to go by boat from the northern part of Argyll to Fort William before changing boats for the canal. I'm not sure whether there were steamers on those routes in 1864, or whether the whole thing would have had to be done under sail.
They couldn't have gone by train because there were no trains to Oban until 1880, or to Fort William until 1894.
Any of those journeys would have taken days in the mid-1800s, and it seems extremely unlkely that you would take a 13-year-old child suffering from smallpox on such a journey, quite apart from the fact that you wouldn't want to have an infectious sufferer on boats, never mind in a coach or on a cart.
Even for a healthy person just travelling from Oban/Lorn/Ardnamurchan to Inverness would have been a fairly major journey, not to be undertaken at the drop of a hat. So there must have been a good reason why John was admitted to hospital in Inverness.