How can I Change the Apple Configuration Signing Certificate?
This is currently how the Apple Configurator works - it doesn't have a provision to load a certificate but instead generates self-signed ones automatically. If I run across a way to hack this, I'll link it here. If you need profiles to arrive with a signed certificate, look into Lion server or another MDM solution.
In practice - you only see the certificate warning when you are sitting in front of your Mac and connecting devices via USB. I'm not sure what additional layer of security a signed certificate can provide in this case. It's not like you are connecting to some remote server when these profiles get installed.