If the bank decides to take away the transfer/ draft capabilities from a money market account due to repeated occurrences of exceeding the withdrawal limitations imposed by Reg D - and items come in for payment, can the bank pay the items against another account that the depositor has with us or do we have to return the items?

I appreciate your help in this matter. Thank you.

I would not unless you have an agreement with the customer to do so.

If it's a Reg D violation why don't you just convert the account to a transaction account?