You should be fine. Just flip the intake around, and get back to business. You'll need to re-do the RTV sealant, though.
Edit to add: And since you have the intake off, it would be a good time to do this little mod.
You use a Dremel (or some other rotary tool) to grind small channels in both ends, where the intake touches the engine block. This helps to keep your sealant in place, so you don't end up with oil leaks at those seams.
[This message has been edited by Blacktree (edited 10-28-2013).]