Unless a miracle happens, I honestly don’t think a guided backpacking trip will be going ahead then, and please, please don’t travel to any part of the highlands until the government gives the all-clear. If you’re booked on the Fort William service (or the Aberdeen for that matter), then that portion will undoubtedly be cancelled then, so your ticket will have been cancelled by default (and your money refunded). If you’re booked on the Inverness service, that portion will still be running but you’re asked to avoid non-essential travel; I believe that even if you have a fixed advance ticket, CS have made it so that you will be able to postpone your journey to a later date this year, so you won’t lose out financially.
CS have suggested that their emergency timetable will continue until 30 May, but the government advice against non-essential travel may last much longer than that and it may well be extended- I like to think that restrictions will be lifted and we will see a Fort William and an Aberdeen service before the summer is out, but this relies on us playing our part now and staying at home until we’re told otherwise.
P.S. I’m afraid your observation that your planned trip is to an unpopulated area is irrelevant in the current climate, as a simple trip/fall could result in a mountain rescue callout and your being hospitalised when the already limited hospitals in northern Scotland are working at full stretch. I wouldn’t recommend going, and would ask to postpone the trip (postpone, though, rather than cancel, as CS and lots of outdoor/tourism businesses will be glad of your business once this ordeal is over).