If your targets are Windows machines, importing certs is easy via either Certutil.exe or Powershell commands. Figure out the syntax you need to do it interactively on one machine, then put that into a custom task and away you go. I’ve scripted the import and export certs on thousands of machines that way.
If using *nix, then OpenSSL commands would accomplish the same thing.
If you take it a step further, it is also possible to script the binding of the certs to IIS or a Java application server.