Instead of scaling the referenced object group it to itself and scale that. The theory of file referencing is that you are not supposed to be able to modify the referenced objects in the referring scripts. This is supposed to preserve the objects in a production situation where many shots are being done with the same models, for continuity's sake. The reality is that I will never again use file referencing after my experiences on a soon to be released feature. While the idea is that Maya would never corrupt the reference files, it did exactly that, about three times a week on my project, if it crashed while writing out files over a network. Since these reference files were models for 30-40 shots that half a dozen of us were working on, or rendering, we all were stopped in our tracks until the problem was solved. I wrote a mel script that assembled shots from the source files instead of referencing, and that is the way I will always do it in the future.
/*Never confuse motion with action*/