I'm guessing you're going to have to position the front wheel so that it is aligned with the rear wheel (i.e. as if you were doing a rear wheel alignment,) clamp it so that it can't move, then loosen the fork clamps and move/twist the handlebars to get them in alignment with the fron wheel (might need to take measurements from the bar-ends to some central point on the bike to make sure they are an equal distance). At that point you can tighten everything back up again.
I'm just trying to figure out how I would do it though. I have had forks off other bikes in the past (to put new seals in etc.) I had the advantage of a "naked" bike without a fairing though, so it was easier to sight down the fork legs and make sure they lined up. Also, when I did it I had the front wheel off which may make it easier as you can lay a straight edge across the fork ends, and grab and twist them if you need to.
Hope this helps (or someone has a better idea.)