I'm not sure about this. I have a feeling something like this would not run in Medium Trust. Though you got it working in ASP.NET, a brief skim of the documentation doesn't make me think it was designed for web apps though it can work with class libraries, it seems more geared for desktop and a stateful event driven system as opposed to the stateless web application. I think it might be heavy to load up all this on a request by request basis.
I also don't see any use I would make of it in the installation system, because I don't want my web code running with permission to modify anything in the bin folder or install dll files there. I like to keep everything read only except the Data folder and let the ftp user account be the one that installs files, not the web process account.
Maybe I would feel different having seen your example code and usage and if it works in Medium Trust. It does sound interesting and I don't want to dismiss the idea off hand since I dont really know much about Mono.Addins, but my gut feeling on this one is doubt.