The teacher in my center even encouraged meditating while walking when I asked. I saw other students doing the same and no one made anything out of it. Same in Japan, where I also sat. Sounds like an unfortunate interpretation at the particular center you where at.
On the other hand, if you're spotted walking slowly back and forth along a line, you'll be criticized for introducing walking meditation. So while Goenka retreats might encourage skepticism (this has not been my experience), they severely discourage experimentation. They are highly authoritarian environments.