Certainly a problem, but as most people now work hybrid, the challenge that extends to rail is to drive modal shift and get those hybrid workers to 'train it' 2 days a week rather than drive. If you can get 2.5 times more people using the train 2 days a week, you're taking more revenue than pre-covid users travelling 5 days a week. Arguably, if it's only 2 days per week, train becomes more attractive, simply because you're not dealing with full and standing trains 5 days a week (and with flexible hours being more common, arguably there's new opportunities to manage numbers and get more bums on seats vice standees).
If you commute 5 days a week, your car mainly sits at work and is an expensive thing to own to just sit somewhere. If you only work 2 days a week, the car is at home more at available for others to use, so it becomes less economic to use the train, and better to use a car. Given the Scottish Government commitment to EVs too, it is considerably cheaper to use an EV.
ISTR a SG committee some years ago examining this and concluding that it was worth supporting not for transport reasons, but tourism ones. They reckoned it brought enough additional tourism to the far north to be worth the money (presumably because a lot of tourists will take trains but not buses). Of course, that could always be re-evaluated.
In most other senses the bus is already better, in that it is faster than the train on this route. However, as I said somewhere upthread, trains have tables and one can work on them. However wonderful buses might have become elsewhere, the buses on this route definitely do not. So the train does provide a real benefit that isn't available on a bus.
The line won't, but that probably doesn't mean Scotrail has to run passenger trains on it? (I mean, if the SG gives permission to stop)
It is, of course, tourists who are most put off by disruption. They are choosing to travel by train, but don't have to. They are most likely to choose not to travel by train too. With large windows, guaranteed seat, seats matching windows, forward facing in most cases, modern buses and coaches, and considerably cheaper, Scotrail really don't help themselves.
Other than sentimental, I can't see a reason for keeping The Far North Line open to passengers. It doesn't make any economic sense. With budget constraints it is an easy win to close it to passengers. I'm not saying it will happen, but I can't believe there isn't an accountant looking at it.