You are running a risk using any antibiotic in your reef, however, Metronidazole (aka Flagyl) may be a safer bet. In human medicine it is used to treat anaerobic bacteria and protazoa - marine ich is a protozoa. I believe Nitrosommas (the bacteria that converts ammonia to nitrite/nitrate?) is an aerobe so it probably won't have any effect on the nitrogen cycle (key word is probably). However, since zooxanthellae, (sp?) although a type of algae, could share some of the same biologic processes as the bacteria to which they are related you could potentially bleach all of your corals.
Praziquantel is used as an anti-helminthic agent (worms!) - don't know if it would do anything to protozoa.
i'm thinking of giving metronidazole a try. but is it better to add it to the food than to the water of the main tank? is metro better than 5-nitroimidazoles?