Hi,
Is there a utility that allows you to pre configure the msi installer of the Etoken pro and let you add intermediate certificates or Root Certificates automaticaly?

Yes, if you r using RTE 3.65 their is an option to Automatically install CA Certificate. Follow following steps to get this option :-
Start > Programme > etoken > eToken Properties > Local Machine > CA certificate loading. select Automatically install CA certificate > save changes.