You already outsource your independent audit function to them so how could there be an independence issue? Unless they designed your BSA/AML program, I think you should be fine.
On the other hand, I would definetely ensure they have the qualifications to perform the BSA audit. Trust me, just because it's an accounting firm and might have a CPA or two on staff, doesn't mean they know anything about BSA/AML regulation. It's an entirely different beast.
Find out if they have auditors that either have a lot of banking experience or some kind of certification and ask what banks they have performed BSA audits for near you. You can always make a friendly call to their Compliance/BSA officer to inquire.