There will be differences in pricing no matter what. Look at Ebay,they are still trading at around $25 dollars there , which is amazing considering what just happened at MTGOX.. That point is irrelevant.
The high prices on Ebay are almost certainly due to the fraud risk that the sellers have. If they are, e.g., paid with Paypal, the buyer can reverse the transaction after receiving the Bitcoins. Therefore, every seller will charge a premium to cover that risk.
On the other hand, the buyers also get an advantage for paying more: They don't need to trust platforms like MtGox, but can buy there coins on a more reputable platform. If the seller does not send them the Bitcoins they can be sure that they will get there money back.