I did try and game this. She leaves early, which I wonder now wouldn't be a fairly common thing. Like, here your underaged magic kid just needs a few years of basic training, then you put them in a "real" school. Especially in a mixed magica/muggle family. I have her like 5 years younger... ? I can't find my notes. Let's say that. So he's a seventh year when she's second. That's a gap with no interaction in most schools. Except for the Prefects and star Quidditch players. I sort of expect by sixth year, Snape was trying to lay pretty low to avoid attention if he had fallen in with the wrong crowd both inside and outside of school. 

If the school is really 1000 (which the numbers don't work from the house-year level, but supposedly) then I can see the younger kids not paying much attention to the older kids in that large of a student body. That's my set of assumptions to make this work. Otherwise it doesn't work. So I can totally see this being a point of disbelief.