Stressyhead, I don't know if you're thinking of somewhere more rural than this, but Crieff Hydro has self-catering accommodation, and is in itself a very child-friendly hotel whose facilities you can use if you are staying in one of their lodges. It's about a 10-15 minute walk into the small town from there. It's not very near Loch Ness I'm afraid, though. There's a lovely child-friendly hotel near Loch Ness called Polmaily House , but it's not cheap. A couple of nights there would make a nice end to the holiday though!
They're the only places I can think of offhand that we have been to; I'm not big on isolated cottages miles from the nearest town I'm afraid