How come the dye has turned purple, how long have you been running it? My friend has the mayhem's red dye too in his loop and his was still red last time I checked (built the loop in september). But yeah, the tubing gets colored (that's the case with all dyes), but that's not something I think is a big deal as you won't notice the colored tubing while you're running the dye in your loop (obviously) and tubing is cheap so we change it few times a year (when working on the parts or just doing some maintenance).
2 pumps 1 loop sounds better imho
But if you were to do separate loops for your cpu and gpu's, would you need to bleed both loops if you were to do some work on one of your gpu's for example?