When you understand a few key points, the system because trivial to exploit.

1) The owner, upon noticing that items are missing, will begin looking around and approach a random party member in sight.

2) The owner will not immediately detect that items have been stolen. There is a period of time where you can get out as fast as possible. This begins a) when the item goes missing in the case of regular theft and b) when the pickpocket window closes.

3) The owner will search only the bag of the person he accuses. Stolen items located in other bags will not be considered.

4) The owner will search only for his own items. Stolen items belonging to other characters will not be considered.

5) The owner will only search a "decoy" party member once. And afterwards, he will very shortly give his items up for lost and return to his original position.

So basically, you get in, steal the items, have your other party members nearby, stop sneaking, and run far away around some corner. Upon realizing he has been robbed, the owner will approach a decoy immediately, as they are in range and the actual thief is not. Allow the search, he will find nothing, and he'll simply turn around a few times in a futile attempt to find the real thief, before finally giving up.

In my opinion, this system of making you jump through hoops and cooperative thievery makes for a much more interesting system.