How long have you been using the filter pad? If it's been more than a month as Lotus pointed out, the carbon is sufficiently deactivated that it won't be affecting the efficacy of the meds. In other words, don't worry about the carbon if the pad has been in use for a while.
When you have sick fish, you don't want to stress them any further than necessary. You're apt to have more problems removing filter media (and risking removing the biofilter) than choosing other alternatives. I never use carbon except in very specific cases.
Keep an eye on the other tanks. If I recall, you did some juggling of fish which exposed at least one other tank to the ich. As a general rule, unless a fish has a very specific illness, you're better off treating whichever tank is exposed since fish share the same water. Also be sure to keep all equipment seperate.