Fiddler2Setup.exe can be launched with a /S
switch (case-sensitive) to install in silent mode. However, it sounds like your goals go beyond a silent installation.
The settings you've described can be set via registry keys; you can configure the settings as you want then look at HKCU\Software\Microsoft\Fiddler2
for the values you want; you could export a .REG file and then import it on the client computers.
Having said that, depending on your needs, using FiddlerCap
or building a custom application atop FiddlerCore
may better suit your organization's goals.
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