You likely got ich because of the stress of the cycling. Ich is pretty much in the water all the time and when the fish get stressed their immune system weakens and allows the parasites to take hold.
I've always treated ich with salt and heat, I don't like the chemicals, but that's just me. Removing the fish won't do anything good for you as you'll just move the parasite with them. Because you are trying to cycle your tank, salt and heat will likely be the safest route to go. Malachite green is good at killing bacteria, along with parasites, and because your tank isn't established it would likely set you back over to the beginning. The link below does a pretty good job of explaining how malachite green works.
http://www.fishdoc.co.uk/treatments/malachite.htm