You'll no doubt get some feedback from someone who has done the entire route, but the last time I was on part of the NC500 (Lochcarron-Applecross-Sheildaig-Gairloch), most of the cars/motorcycles which were traveling in convoy were traveling clockwise.
I'd say that no matter which way you go, you're going to encounter NC500 traffic. From the times that I have made all or part of that circuit, clockwise has been the more scenic way. For one thing, you'll be on the left side of the road (on the two lane parts of the circuit), which opens up the sea views. Plus, if you suffer from vertigo, you won't be hanging out over the edge of the drop off as you tackle the Bealach-na-ba. :)
Now that NC500 drivers are hearing that it's better to travel counterclockwise, they're probably figuring that they'll travel clockwise to avoid the traffic. So just go the way you had originally planned, take your time, and enjoy the magnificent scenery.
And be sure to make accommodation arrangements ahead of time, as if you're traveling with family, there's not a whole lot of accommodation between Lochinver and Thurso.
Best wishes for your travels!