On bitcoin exchanges, such as Mt. Gox and Bitstamp, there are multiple bots that buy and sell bitcoins at the same time cluttering the markets and the rate of bitcoin. The purpose of these bots is to gain profit, so traders will get more more tempated to start to use some kind of homespun trading bot. What will we see in six months? War of bots, that rally the rate of bitcoin and make markets completely volatile? That defintely isn´t good for the arising bitcoin ecosystem. So if the bitcoin exchanges want to be trustful, the bots should be banned, or should they? 
I definitely don't think that trading bots should be banned. IMO, if Bitcoin is going to prove to be a longstanding, viable, economy, then it's going to have to withstand things like trading bots and not really be horribly effected by them.
Full Disclosure: I'm developing a trading bot.