Well I think part of it was a mistake by the production team that someone in post mixed up and it stuck. Although after watching both the original Tron and Tron:Legacy I think I have to prefer the Legacy style of coloring over the original - for one I think the all black bodysuits with the different colored wire sections was just more striking visually and I think had they been able to do the same EL wiring in the 80s I'm pretty sure they'd go back and do the same thing - as evident by the fact that all of Sam's "vintage" Tron toys and merch is black with the color - so I think by Legacy it was either retconned that the black and blue/white for good and black and orange/red for 'troops'/bad was always the case. With white and blue suits being for either 'older' programs brought into the new system like Zeus and the Sirens or simply 'support' programs and black for the other programs that did day to day stuff.
The Tron Uprising cartoon sorta makes it harder since there are some programs with pink and purple and green and orange too.
What I would still like to know is - when Quorra came over into the real world, did she come over in her Grid outfit or, since she clearly wasn't from this world, came into the Arcade naked? Not that they'd stoop to it, but I've been curious as to how Clu's forces would come over if they figured out how to cross over. That quasi fan film with the return of Sark and his bike he came through just as he was in the Grid.
I'm really actually looking forward to more Tron movies - I think Legacy is turning out to be one of those movies that I watch whenever I see it on FX even though I've got it on DVD and digital and I've seen a number of times. It's just so striking. Even though the story is pretty thin