I agree with Patrick. There's nothing special about a short sale that would prevent your acquiring clean title. During a short sale, your contract is still with the seller, not the bank. The seller and his/her listing agent must work with the lien-holding bank to come to terms, which is often sticky, but your contract is not with the bank. Before you REALLY have a transaction to consider, the bank must agree to terms, including the amount of any commission to a buyer's agent.
Because lenders can say yes/no at just about any time, you really need an experienced agent who can construct an offer that protects your interests. They usually have to work for less than their normal commission, so take that into consideration. Regarding your concern about being able to sell in the future or being beholden to someone, know that if/when you close on this transaction it should belong to you wholly and completely. Once you know who the lienholders are and have agreements from them regarding payoff terms, you should be clear.
FYI It's really a good idea to have a buyer's agent whos experienced in short sales. The lender, not you, pays their commission, and no, you most likely aren't going to get it for any less money by doing it on your own.