Let's think about this: the manifest file launches the deploy file launches the executable, I think the error message is coming from the deploy file as the executable cannot run without the proper framework. Thereby the answer to your question would be no in a traditional sense.
Of course, you can use an existing app or service to customize that kind of error message, but you'd be stuck deploying that system as well. What I don't get is my clickonce apps install the framework for you resolving the problem themselves, if yours don't for some reason, I'd recommend putting an executable of .NET 4 FW on a share and linking people from there.
Another hackish way you can do it, is if your setup is like mine, you have a web page that clickonce installs off, maybe you could check in that web page? You'd have to change from .htm to .aspx, but that's not a problem on an iis server.