Rebex Secure Mail doesn't support extracting certificates from Active Directory. However, this can be implemented quite easily using .NET's System.DirectoryServices assembly. I have found what looks like a simple example code here.
NOTE: The example code uses X509Certificate2 instead of our Certificate object, but this doesn't matter – you can replace X509Certificate2 in the code with Certificate, but this should not be necessary because Certificate has an implicit conversion operator, which means you can simply supply X509Certificate2 objects to methods accepting Certificate objects.