I have been in this situation many times. In one place, we simply had the customer move to antoher area that did not display any FDIC items but rather the insurance pieces. In the other instance, we used the same office but removed the free standing FDIC stand and as we did so, explained our actions to the customer, which helped them grasp the understanding that the two were not connected.
If your employee does a good job of ensuring the customer understands the differences, you should not have any problems.