It really depends on your goal. Do you need telephony interface card on the server? If yes, there might be some legitimate need to run Windows native if you must. But then, stability of native drivers could be a problem. Otherwise there are plenty of alternatives to use Linux without pain. As others mentioned, there are out-of-the-box stuff. If you simply can’t live without Windows, check out ready made Astereisk appliances under VMWare.
You probably haven’t explored Asterisk Windows port much. (Gotta admit I haven’t touched it.) I doubt there is much difference if all you want to “develop” is an IVR. You still deal with config files mostly.
I seriously doubt if you will find C# very useful for an IVR after playing with any flavour of Asterisk for a few months. Yes you can use C# in AGI to implement a full IVR, but what’s the point of having a (robust) PBX platform if you do so? IVR is one of the strong hands Asterisk plays. Writing plain config files (not to mention AEL) is 100 times easier than debugging a full-blown AGI application, whatever language you use and however proficient you are in this language.
As others pointed out, the steepest learning curve involving developing IVR on Asterisk will be Asterisk specific concepts, syntax, variables, functions and applications, not Linux. If this is of any comfort, you can ask a kid off the street to configure a Samba server (most likely installed by the Linux OS) pointing to Asterisk directories so you can “develop” config files in a Windows editor (hopefully not Word ) and drop it to Asterisk. (Well, WinSCP could do the trick as well.)
Once you realize that writing the entire IVR in AGI is not worth it, you’ll also find little advantage in C# compared with any other C-family language you can develop in your favourite Windows based IDE (say Visual Studio). Turn on ANSI flags and your application can be readily deployed on Linux. For the amount of AGI that you may need to write, you won’t be missing any non-ANSI features.
If - just in case - you are comfortable with Eclipse … What’s the difference, at all?