If I misunderstand your question here please let me know.
Because you mentioned you have new merge module but update the dlls it not easy, so you want to get an installer for that. So I think you can build an installer project, just need to reference the merge modules and you can build an installer which contains the merge modules you need. Then you can run the installer in your server, just like you did in your product installer, it just be a very simple one.
And if you don’t need that you can download the http://wiki.thinkgeo.com/wiki/_media/mapsuite10/mapsuiteruntimedependencies.zip, it’s also be an installer, you can directly run it.
I checked with our developer about it again, in our wiki page, the merge module hadn’t been updated to the latest version, but the link I listed for mapsuiteruntimedependencies.zip is the latest one. The included dll get changed, we added some dlls into it because some machine missed them and will met exception in certain scenario.
If update them is hard for so many server, I think you can did a test in one of your server to see whether update is necessary for your project.
In fact I don’t have a good suggestion about how to quickly update in so many machine, but I think you should have the requriement to update other package version in these machine, maybe you can update the system dlls when you data other packages the next time.