My best advice would be to try to postpone your vacation, if at all possible. Normally a walking boot is in place for about six weeks, and even at that, your wife's good leg is going to be stressed out from the extra pressure put upon it.
Edinburgh is a very hilly city, and involves a lot of walking. You can take taxis from place to place, but one of the joys of Edinburgh is walking everywhere. The museums and the castle also involve a lot of walking. Portree is also hilly, especially if you're heading down to the harbor. Skye does have some hikes that don't involve a lot of walking, but most of them do. You could take a couple of boat trips out of Elgol - AquaXplore have landing and non-landing boat trips. You may want to take the cruiser rather than the RIB, as it has onboard toilets. You could also take the Bella Jane for a non-landing trip to Loch Coruisk, or a 1 1/2 hour landing trip, if your wife feels that she can negotiate the jetty steps at the Loch Coruisk landing. There's probably a video somewhere of the steps.
There are some scenic overlooks on your way from Invergarry to Skye, so that wouldn't require too much walking from the car. Many of the castles which are along your proposed route involve not only walking from the car park to the castle, but also negotiating steps and staircases within the castle.
If there are any Highland Gatherings scheduled during the time you're in Scotland, that would be something to enjoy without a lot of walking. Also short walks/hikes to scenic sights like waterfalls and overlooks would be another possibility. Many, like Mealt Falls and the Kilt Rock on Skye, have a car park right there. The Fairy Glen would be another possibility, if you can park close enough.
I don't want to discourage you, as I love Scotland, but it's a very "outdoor" country, and to get the most out of it, you really need to do a great deal of walking. If your wife feels that she's up to it, by all means go for it. But I'd follow the advice of your physician(s) regarding whether the boot should remain on her leg while you're in Scotland. You can get free medical advice from health clinics while you're in Scotland. Your hotel/B&B would know the location of the nearest one, should you need assistance while you're in Scotland.
Very best wishes,
p.s.: If you're anywhere near Mallaig on your way to or from Skye, you may want to take a sail on the Knoydart ferry operated by Western Isles Cruises. The best non-landing trip is the 2:15 out of Mallaig, which stops at Tarbet on Loch Nevis on its way to Inverie. It's about a three hour tour (with apologies to the S.S. Minnow). You'll get to see some parts of Scotland that are almost inaccessible without lengthy hiking.