i'm in your conscience
I wouldn't think that Pokerus being from a hack would make the whole Pokemon illegal, personally. But I'm not totally sure about that. I'm just kinda thinking that if the Pokemon was caught legit and you EV'd it legit even though your Pokerus was from a hacked Pokemon, then it should still be legit. Because Pokerus or not, EV training will always result the same way in the end. Pokerus just makes it faster. So I wouldn't really worry.
You might consider asking in the shoutbox on Pokecheck, but iirc, they're a bit mean and strict in there to where if your question isn't strictly related to Pokecheck, they're rude about it and tell you to use Google or mute you or some crap. So...well yeah maybe don't ask there in that case haha.