Everyone should collect how they want. It's one thing to to prefer your own method of collecting over another, but it's another thing to look down on someone else who collects differently than you.
As far as the stigma for repro labels goes, I understand why some people think it's bad for the hobby because at times, it can be difficult to tell the difference between an original label and a fake. But I don't feel that stigma should apply to game covers, especially for games like NES, SNES and N64 which never game in plastic cases with printed covers. It's only come up one time for me. I had a picture of some of my NES games in Shadowfox cases posted on facebook and one person said he didn't like them because he doesn't like repro boxes. I explained to him that they weren't boxes, but plastic game cases that could never be mistaken for the real thing. He response was that he couldn't tell the difference, and therefore, it was bad for the hobby. I told him that if he couldn't tell the difference between a cardboard box and a plastic case, the video game hobby might not be for him.