The command line tools are easily installed from within Xcode -> Preferences -> Downloads or by downloading the .dmg from Apple's developer website and installing it by hand. Neither are the end of the world.
Rather than distributing two copies of the tools (one with Xcode, and the (awesome) new CLI only tool distribution), they DRY it up and have one canonical package for everyone, reducing testing, packaging overhead, possibility for divergence between the two packages, etc, etc?
The tools are already available, just not in the normal path locations. Also if you are modifying the files installed by the CLT installer such that they get messed up you are doing it wrong.