I'd say that there is always going to be an adjustment period. I understand why the Sharks have set-up that way. I don't think PP's have a tradition point shot guy anymore. They basically all run a dynamic 1-3-1, with the defender walking the line and a guy on each half-wall. For example, using the team I'm most familiar with (Leafs), the Leafs run their PP through Marner on the right side, and want him to use his vision to either set up slap passes or a deadly cross-ice path to Matthews. I don't think it would make sense to flip Burns and Karlsson though. You want Burns to receive passes where he can utilize his one-timer, even his wrister is probably better coming off the left. So, if you can re-jig things so that Burns takes the left half-wall and Karlsson is the 1D in the set-up and walks the line, that works.
How exactly are the Sharks setting up? Who is the left-half wall, the net crasher and net-front presence in the 1-3-1 set-up with and without Thornton?