I know its been two weeks since an update on this, but I thought I'd comment as I have a similar setup.
We have 3 Cisco Controllers, and 1 recently installed Aruba, all using Clearpass/Amigopod for guest.
Regarding Wildcard certificates, I can confirm that they work on Amigopod/Clearpass.
I can also confirm that I had absolutely no Luck whatsoever, getting wildcard certificates to work on the Cisco Controllers at all. I did not attempt on the Aruba Controller.
In my setup, the Cisco Controllers all use the same certificate, and I purchased a seperate certificate for the Aruba Controller. Just make sure on both setups that you go through the steps to combine the Purchased Cert and the Intermediate Certificates into the same file and you should be fine. There is some pretty good documentation out there for doing this.
Also make sure you do what "gbenedict" suggested regarding DNS and the resolving of the names. and you should be good.
No Certificate issues here after doing all of that.