Just copy them; you should be able to do it silently.
Most applications do not really require installation, unless they do something special to the system. Often they also introduce some new "file type" or suggest to register existing ones to be handled by the newly installed application. This is often not really required, or can be trusted to the user. Also, one good way of making required modification of the system registry is doing by the application itself on its first use.
To me, the applications which do not require installations are the very best. A while ago, Microsoft started to encourage this kind of installation — finally. Especially for .NET products. This healthy trend is now growing. Some products coming with the installer are often come with "portable version" which is used immediately, without installation.
But it you still want regular MSI installation, you just need to make it silent, using regular Setup project; I don't see why not.