It depends on the definition of legit.
If legit is "not interfering with the game data in any way", then no, piping's not legit, because piping is a way to reset the monster values over and over until you get what you want. In that respect, the only way to be truly legit is to just take what comes, when it comes.
Personally I don't hold with the legit/unlegit thing because of the grey areas. Is it legit to hack back a weapon lost to FSOD? No? Why not, when you had that weapon before and saw it drop? You already
owned that weapon. An argument could possibly be made that piping a rare monster is actually less legit than ARing corrupted data, since in the one instance you'd already gained that achievement whereas in the other you hadn't.
I ought to stress that I'm not speaking up for either side here

I have legit characters and I have unlegit characters, leave it at that.
As for piping, though... I don't do it, but not because of legit/unlegit worries. I don't do it because it makes my gamecube make frightening noises. PSO's hard enough on the lens as it is. The benefit of doing runs is that you're gaining exp while you play, and your cube isn't having to do all that strenuous loading all the time.