I know nothing about running, and little about shoes. But one thing struck me as obvious:
Wouldn't the danger of injuring your feet while running increase if you were wearing shoes that didn't fit? It seems as though you would wear out running shoes before you changed size. Even if you did change size, you should wear the very best fitting shoe you could find.
I started running a few years ago, and if the OP was planning to use the shoes for running (vs. every day sneakers), I can see where the clerk is coming from. Feet swell when you're running - I don't buy shoes that are uncomfortably loose, but they have to be roomy or else my feet will be pressed against every inch of them by the time I finish my run. (And let me tell you - this can cause some painful damage that takes a while to heal!) Several of the running stores I've been to recommend buying running shoes slightly larger than your usual shoes. However, it sounds like the pair the OP had were already plenty roomy.