Hello, and congrats on your engagement! Obviously I don't know what your budget is, but you can hire the tiny, old chapel in Edinburgh Castle for £1000-£2000. It holds about 15 people max (from what I remember) and so simple and gorgeous. Then you walk out and you're greeted with a view of the whole of Edinburgh, stretching out to the Forth, it's stunning.
There's also a chain of small hotels in Edinburgh that do weddings, www.townhousecompany.com, very personal. If you get married in Edinburgh there are plenty of places for nice pictures like the Botanical Gardens. Edinburgh Zoo also do weddings now I think! Have a look here: uniquevenuesofedinburgh.co.uk
Outside of Edinburgh, I'd suggest googling Grampian Wedding Directory for places in the North East. Again, depending on budget, there's Guthrie Castle, who despite being a big venue, do a lot of small intimate weddings as they have a chapel in the castle itself.
Those are the two geographical bits of Scotland that I know, I'm sure someone else can recommend venues in other areas!
(oh, thought of somewhere else - Loch Rannoch hotel has beautiful views and is licensed for weddings)