@JimSkim You can run the accelerator over HTTPS. You would just configure SSL like any regular web role. You may want to put the admin portal on a port other than 443 though otherwise you will not be able to use a different cert for any host sites on the accelerator. The other option is to use a cert with multiple domains.
You should also use SSL when doing webdeploy to secure your credentials as well. This should work by default.