Hello Nico,
I am not familiar with the cllick-once programs as you describe them here.
But if you need to run a software deployment with user-credentials, did you try to create a user-configuration to install software?
From Software Deployment - Packages, you can create a config via "Install Software - User".
In the configuration you can specify which user account should be user (i.e. "Target User").
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By Office 2013 I guess you are talking of Office 365?
Yes, this can be modified by con deployment tool but installing it requieres administrative rights, so that is not a good example when you need to run a setup as user.
I guess of course that users to not have adminstrative rights.
In the end I am not sure what kind of "setup" you want to run for users unless they have admin rights..?
