I dont think there are any applications that will show you as offline even tho you are online. If that was what you were asking.
One of my real ID friends sent me a message the other day saying "Man I swear it seems like you are a bot sometimes you stay up so late" I then deleted him from my friends saying RealID caused me to lag...
you have 2 options: being paranoid and not trusting your friends with your secret telling people that you bot that's about it I like #2 & no one really cares. Other than when the raid leader needs something like a guild achievement (ie: I was 'forced' to take 10 of my bots off of farming about 1 month into cata to farm 10,000 fish pools for our guild achievement / cooking recipe - needlesstosay - we had the achievement and recipe in a couple of days)
rofl kickazz, we spent two raid days for doing that achievement with all 35pplz in setup. botting with 10 chars is another fine method.
I don't farm on any of my toons that people actually know. And NEVER liked that realid crap, so i have noone on that list.
You can actually disable RealID ingame by blocking a port with Windows Firewall. I enable the rule every time I bot, so it shows I'm offline to all my friends. Pretty sure guildies can still see you though. To do this just make a new rule in your firewall blocking outbound access to port 1119. It's extremely easy to toggle on/off with Windows Firewall. P.S. - Make sure to enable the rule after you log into your account, or else you won't be able to connect to the server.