In reply to no_more_scotch_eggs:
There is a railway station in Blair Atholl. You could take the train and not have to worry about where to leave the car?
There's a car park at the visitor centre that I think doesn't have any overnight parking restrictions. There is a reasonable amount of traffic through there because of the visitor centre, the park next to the river and the chipper. Or there's a patch of ground next to the Atholl Arms (where you turn off for the railway station, in fact) where it looks like you could leave a car for a couple of days without it being in the way - and being next to the busy hotel its more likely that untoward activity could be spotted.
T'other side of the river in the village itself I doubt you'd have any issues leaving your vehicle sensibly parked on one of the side streets but still nearish to the main road. Whether passing traffic on the main road would be a deterrent to n'er-do-wells I couldn't say but as Mike-W-99 says, it's not exactly a rough area.
You can reduce the chances of attracting the attention of folks with malevolent intentions by making it clear that there's nothing in the car: glove box open and empty, rear sets folded down and nothing in the boot etc. (Not such helpful advice if you do intend to leave stuff in the car that can't be tucked out of sight beneath the seats, though.)
