Is it dangerous to reinstall 10.7.4
Reinstalling the OS just for Safari seems a bit drastic. The reason it says that is probably exactly because you used rm -rf as opposed to dragging it into the trash.

In OS X there is a central registry of installed applications, and afaik when you drag an application to the trash, it is automatically removed from this registry. When you just rm -rf it will delete the files but not the entry in the registry.

So I'd try : reinstall Safari 6 normally, then drag it to the trash. This should remove it from the registry, so try to install Safari 5 afterwards.

If it still doesn't work, try using the /System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister tool to manually unregister Safari.