We've had folks on Mag since the beginning (or nearly) with "spy" accounts in alliance there. There was also an alliance druid that had a horde spy account and would use him to track lowbie zerg groups and harass us. Neither ever got banned for it.

With regards to other uses of alts on the opposite faction, there are two things that I know can get you banned:
  1. "swapping" honor kills by trading kills in PVP
  2. Transferring large amounts of items from faction to faction via the neutral AH. It should be noted that if you use these items to equip your characters, no harm no foul. If you do it with the intent of jacking up prices or making money because one faction has a surplus of an item, that will get you banned.
I wish I could give you links to the blues that have posted about it but it's been a year or so since I really cared about this stuff and went researching it.