how to prevent modification(deletion, rename) to an assembly?

Don't the operating system and the CLR do it for you? I thought unless you did something esoteric like Shadow copying and stuff, you won't be able to modify loaded assemblies?

.NET does not provide that type of security. You must rely on the normal operating system permissions for files and folders. In other words, it must be installed by a different user (perhaps administrator), the user must not have the same permissions and cannot be administrator, and the file must be marked read-only. If you are trying to prevent the user from modifying files they install themselves, there is no way to do that.