Do I need to stop the transport service to remove this certificate?

A special Rpc error occurs on server SERVER: The internal transport certificate cannot be removed because that would cause the Microsoft Exchange Transport service to stop. To replace the internal transport certificate, create a new certificate. The new certificate will automatically become the internal transport certificate. You can then remove the existing certificate.

I actually just removed it using the IIS applet and it has disappeared now.

I restarted the transport service afterwards and it started up OK so I assume this is an acceptable solution.