There are ways to do what you want, but they are not necessarily the best ways. If the controller goes out of line of sight of the remote, you are going to have to use one of those wireless devices that converts the remotes signal to radio waves (to send it upstairs) and then back to infrared when it gets there (to make the box read your instructions).
I've tried one of these in the past, and it worked o.k. most of the time. There are even some that apparently work very well. I'm a bit of a "purist" when it comes to such things, so I would exhaust every option to somehow route the cable up to your attic before going to these wireless options.
CBS construction can really limit the options of running wires after the home is built. But some walls may not be block and you might have a path to your attic through these (by dropping the wire down from above). If your setup is such that all nearby walls are block, this does create some issues. One option might be to take the wire outside (through the block), run it up to the attic wall inside very thin plastic PVC (conduit) and then back into your attic. I don't know the specifics of lightning risk with this, but these rotors are generally thought of as being used as outdoor devices, so the cable can be set up to run outside (consult with a knowledgable electrician for any specific issues). If you do it, you can paint the PVC the same color as your house and it will blend in pretty well. The rotor cable is very thin- I'd say about half the diameter of RG-6 cable (at most).
If that won't do, I've seen lots of these wireless devices and picked up one set from...http://www.smarthome.com/wirelessir.html
...though I know some of these are available locally from the Shack, Best Buy, Circuit City, etc. Again, the one set that I tried worked pretty well for me, but they sometimes would miss a signal. With this rotor, you won't have a way to specifically know that it missed a chunk of the channel unless you go eyeball the antenna or go up to your attic and look at the channel indicator on the box (a clue will be that the signal doesn't come in or that the strength meter is not as strong as usual). I imagine you having to check too often such that it might become a bit of a pain. But, ultimately that's up to you.
I hope this is helpful. If I can answer anything else, please let me know.