I'd argue that calling a VBS from the command line is much less manageable than using CLR. Calling VBS from the command line introduces points of failure that don't exist in CLR, and it also introduces a possible security hole. Unless you already have the operating system extension enabled, I suggest you keep them disabled. CLR is much more secure.
The CLR doesn't have to be in C# either, it can be in VB. And, as you see, it's very short. Personally, I keep my CLRs under source control, and they are very easy to manage. Once deployed, I don't usually have problems with them at all...
It's ultimately up to you and your boss what you do, but personally I'd try to make the case for the CLR. Relying on the operating system seems sloppy, especially when the database provided the mechanism to do what you're doing, within the system, without compromising security.