assuming the flip flop is fixed/fixed(room for a lockring with backthreaded lockring mounts on either side) you can, but the shop probably has heard bad stories about it not working out... it probably wouldn't be a problem, but having half the threads is definitely a concern, if not an issue. they don't know how you're going to use the bike, and they don't want to do something that's going to cause an issue. then again, if they tell jamis that they did it in accordance to jamis' site, maybe it would be okay.
unless you're really beating on it, or your sprocket has a failure or problem down the road, you probably won't ever run into an issue with running a freewheel on the other side- but i totally see where the shop is coming from, not wanting to go ghetto. the proper way to do this is simply replace/redish the wheel with a true fixed/free hub.