It seems like it would be possible using ssh or alternately using cscript or wscript. I've done some stuff like that before (to recycle servers on a windows box for example). The only issue with it is that some of the scripts go off and never return (forking processes). (Not an editorial comment btw).
You would have to push the key file to the server using robocopy (or the like) or scp then execute the command on the remote server to import the file into the specific java keyfile using keytool I think. Let me know if you want more info along these lines.
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