.NET Framework doesn't works like that. If your program needs 3.5, no matters if you install 4.0, it won't run. Because it needs the libraries that have that version.
You can install on the same machine .NET Framework 1.0, 1.1, 2.0, 3.0, 3.5 and 4.0 and all of them will be handled individually by the OS.
BTW, a new version is out, you should uninstall EF, check in your CoH folder to make sure Eastern_Front folder was wiped out, then download and install it. There are a couple of updates for 1.30 version now but should be downloaded by the launcher.