Reshiwott, I did some research, and after being online for awhile I found out you were right.... to an extent, the azure flute cannot be obtained legally, However even if the flute was hacked, Arceus is still legit. Much like when you breed a hacked pokemon, is the baby hacked? or legit? (The answer is legit) here is yet another quote from another site to back up my statement:
"It won't affect the Pokemon directly as far as stats and stuff go and will for all intents and purposes be a legal Pokemon, the only "illegal" thing you did was hack an item that can no longer be gotten is all"
Edit: This also means if you put it through a hack check, it should come out legit, which should be proof enough.