If an exempt employee is allowed to go in to the negative on leave time and then that employee is terminated, does he have to pay back the money for the negative leave time?

It really depends on how the leave policy is written. Some employers allow employees to borrow leave time from future accruals, with the intent the employee will stay employed at least long enough to satisfy the arrears. When the employee leaves before the arrears are satisified, it is likely the employer will require reimbursement, usually deducted from the last paycheck. The employer attempted to accommodate your need for more leave time, so it is not uncommon to have that money repaid to the employer if you leave before it is earned.

So as long as we have in our policy that employees are allowed to be in the arrears in leave time but this must be paid back if the employee leaves the bank, then we should be covered?

That is correct. Make sure the employee understands this and signs an authorization to allow the deductions to be made. Normally you should have a signed authorization as part of the employee's new hire package to cover this as well as any loss of funds that can be proved.

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usually deducted from the last paycheck

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I should add, deductions can be made from the last paycheck only to the extent it does not result in the employee being paid at less than minimum wage for the period of pay calculated.