When Blizzard launched the web interface to the auction house, they also exposed a bunch of JSON accepting/returning URLs that implemented searching, buying, and selling. The URLs and their parameters were easily reverse-engineerable from the web Auction House's javascript.
I had to log in to that account once or twice a week to manage inventory space, but other than that it was autonomous. My trading account was flagged only twice - once because I mailed a large amount of gold to my main character, and once because I intercepted some items that a gold seller was using to launder hacked gold.
In short, Blizzard's involvement with their economy is entirely focused on policing RMT. They don't care how players manipulate markets.
Did you hit the gold cap, and do you still run the programs?