There are major conflict of interest issues with an exchange that itself is a trader.

A real exchange doesn't care what the price is. They just make money on transactions. There's no way they can lose big. The same is true of brokerages.  (Mt. Gox is both, because it holds customer funds.)

It's so tempting for brokerages to trade for their own account. Historically, this is a bad thing; many brokerages have collapsed doing that. It's also possible for brokerages to cheat their customers in many ways.

One is "front-running". A player who passes along orders can insert their own orders into the stream. All they have to do to make money consistently is to occasionally put in their own matching "buy" order when someone sends in a "sell" above the last price, and fill their own order first.  Conversely, they can put in a "sell" on a downtick. The edge from that information advantage is enough to insure profits in a volatile market.

Another is failing to segregate customer funds from the brokerage's own funds. Legitimate brokers are required to do this. (Banks are not, which is why banks are so heavily regulated.) If funds are segregated, and the brokerage goes bust, the customer's funds are still there. Failure to segregate funds usually means the broker is speculating with the customer's money.  Mt. Gox is opaque enough that we don't know if they're co-mingling funds.

This is why I strongly suggest not keeping funds with Bitcoin "exchanges". Move out all balances daily. Trade if you like, but don't use an exchange as a bank. They're acting as banks, or at least non-bank depository institutions, but they don't have the regulation or auditing required to hold the funds of others.