I don't think there are any strong on-the-road reasons to pick either direction. Wind isn't much of a factor for most of it.
Don't miss the Jasper to Lake Louise section, though - that's the best part!
Heading out on the Seeley-Swan (Hwy 83) is way better than staying on Flathead Lake - but if you have to ride Flathead Lake use the west side. Try to go through Glacier National Park.
Come to think of it, if you do go that way, there's a slight bias for going north to south as that would put you going over Crowsnest Pass in BC west to east, which is with the wind. There's a (west) wind farm at Pincher Creek. That also puts you going over Going to the Sun highway east to west, which I've heard is better. I did this the other way, though, and loved it (apart from the west wind on Crowsnest Pass), so really I guess it doesn't matter which way you go.
Really you just can't lose with that tour.