The loss of color is really the least of your worries if your fish are being exposed to ammonia. I'd say that after you get the biological filter back on track, you'll see their color return. I don't know what kind of pellets you're feeding, but pretty much any pellet is going to be better than feeder goldfish!
Keep testing your water and doing water changes as necessary to keep ammonia low. Pretty soon, you'll see nitrite, keep going, and keep it low. It's going to take longer because you can't let these "spike" as you would when cycling normally, so just be patient and keep doing water changes. Here's an article on the cycling process, just in case:
http://www.wetwebmedia.com/FWSubWebIndex/fwestcycling.htm
A beneficial bacteria will help, but be sure and buy one that's not just crap. I like Dr. Tim's One And Only -- it's pricey, but it actually works. I've heard good things about Seachem Stability, but never experienced them first hand. Another idea is adding seeded media -- media from a tank with a functioning biological filter. For now, until the tank is cycled, feed as sparingly as you can.
Either way, wait until you get ammonia and nitrite to zero and have nitrate until you worry too much about their color. And keep up with the pellets -- it's really so much better for them. Also, I'm not that familiar with Piranha, but I'm guessing they'd love some cut-up squid and shrimp, which do great things for my RTC's red color, so maybe they'd help your guys as well.
