It is harder on your transmission, however you can do it. If you dont want it to spray during shifts you do one of the following things: 1. Buy a window switch which you can set a "window" to which the nitrous will spray or 2. You can just turn the nitrous off manually around your shift points.
i would say just go with a push button set up for your nitrous so you can control your nitrous delivery. WOT( wide open throttle) nitrous systems are usually used with manual transmissions because your never on the full throttle when shifting.