This is a very very good question. There are solutions, but probably is not perfect. The fact is this customer should really not belong to your group. In this case, the best approach is to remove him from your group. You should ask him to logon the sub-account your created for him, ask him to update his email address if he has not done so. He will need to confirm his new email address. After that, you can remove his account from your group. The customer will become a regular DriveHQ user.
Since you have only a few employees, you can use our regular folder sharing feature to work around this issue. When you share a new folder, don't share to the whole group, but instead share to individual users. You can create a Contact Group to include all your employees. This way, when sharing a folder, you can select all emails at once.
Another way is to sign up another group account; so you don't mix your customers with your employees. You can connect the two groups by using DriveHQ regular folder sharing.