I can't imagine that this could count against your credit in any way. You've paid a debt you owed. Congratulations on being in a financial position to bring the cash. Many, many sellers are not so fortunate these days. I'd count that as a success and move on!
1. You may need a new agent, this isn't too difficult of a question.
2. Tim is right. I see no reason why the bank needs to know that you're bringing money to the table. All they know is at the end of the transaction they get paid in full. The Escrow Company/Escrow Attorney will write up a settlement statement that will tally up your debits and credits and give you a final figure that you will bring to closing. Meaning that you don't have to come up with money out of pocket until the buyer's mortgage (or cash) has been received. If you are paying the note in full, there is no reason to believe they would record it as a short sale.
Keep in mind that your contact at BOA may have no clue what they're talking about.