Method 1:
If your case is, you don't want the user to see you online, then I don't think you can achieve the same from app. Probably in the desktop version you will get the option where you remain offline to a particular user, even though you are being shown online for other people in your friend list.
Method 2:
Try 'Clear Data' and 'Clear Cache' by selecting the app from "Manage Applications" list in the settings.
If no luck when all the data of your messenger is reloaded, try uninstalling then re-installing the app.