If Hillel and Shammai (as individuals) disagreed on only a few cases (which way to light is NOT one of them), then they must have agreed on this issue. One lights candles each year. How is possible that Beit Hillel and Beit Shammai disagreed on this issue? Are we talking about a disagreement that took place many generations after Hillel and Shammai died so that the people didn't actually see for themselves which way Hillel and Shammai lit? What about a very short term Mesorah?
The basic halacha is that one only needs to light one candle per family, which is what people may have been accustomed to doing. Beis Hillel and Beis Shamai are disagreeing over what is the ultimate way to fulfill the mitzvah (mehadrin min hamehadrin). It is quite likely people had not lit in the ultimate fashion for years - or perhaps, never since the Chanukah miracle itself.