|Rather than taking sides, this is a matter of taking action. Although it is not convenient, you should seriously consider replacing this employee.|
If you have a policy manual and then make side deals for specific individuals, you don't have a policy manual at all. You have a suggestion manual that provides suggested behaviors and not much more. If employees can get away with breaking one policy, the message is that none of the policies need to be taken seriously.
Secondly, since you have terminated employees in the past for breaking this rule, there could be some complaints about favoritism and inequity. In addition, you should rethink what it means to be one of your best employees. This individual has been cheating the company, and her behavior is a form of theft. She has broken a bond of trust, and it is going to be difficult to believe much of what she says in the future.
Although she is difficult to replace, step back and take a look at what you would actually be replacing.