Only problem with using AutoIT is getting it properly synced up which means absolutely no AFK and having to abort the run if it's out of sync. I can't imagine getting it synced right is very easy and the time expended makes it seem like it would be faster just to run the thing yourself. From a botting perspective, it's definitely doable as I'm sure it not that hard to get the timer information from the game and perform a string of actions (move left > shoot lasers > fire missile > move right), but it's like building something for an entirely different game while I'm sure a lot of the methods they used for Honorbuddy and Ryftomate were portable to SW:TOR.
Also, this would be fairly challenging to write a profile for and would most likely have to be a rigid behavior released by the developers for each mission, which if BioWare does a simple query on your recent space missions and sees that you ran Jabiim Escort 35x and each time you killed exactly 77 enemy jets and 32 turrets, that looks very very bottish especially when a few hundred other people have the same stats. The only way I could think to avoid this is to have multiple "runs" and/or a record feature and the run used is randomly selected at the start of each mission.