I have the exact opposite opinion. I want the OS to be as minimal as possible. That way you only have the added stuff if you actually WANT it. If you keep adding stuff to the OS so you don't have to download a new app(is that really so hard?) then you end up with things like TouchWiz. The running in the background part isn't even a real issue because even if it is in the OS something is still happening in the background. What does it matter if it is an OS process or a 3rd party app that is doing the work in the background? It's still happening either way.
But adding more options and selections in the OS doesn't slow down the overall OS much. It's not introducing a brand new service. For example, the LED notification service already exists. It just lights up as white light only. No customization. No color, no intervals, etc. CM doesn't take any more RAM to run than AOSP.
TouchWiz is more than just additional features, and actually doesn't offer you the level of customization I'd like. TouchWiz is also a theme that increases the # of drawables and changes graphics, etc.
Adding options is NOT the same as TouchWiz.
For example, CM's native LED control is less resource intensive than LightFlow, and eliminates a background app that possibly gets killed and ruins your notifications. CM's brightness control curve eliminates the need for Lux, which is another app that must run in the background. Init.d scripts for custom kernels eliminate the need for custom kernel apps like FKU or fauxcontrol.
The point is there are values in the system that already exist, and by not offering those checkboxes and options in the system UI itself, you're forcing the user to install a 3rd party app which takes up RAM and system resources, slows down boot time, just to add functionality. I'm not saying that Google needs to replace every 3rd party app--just to add a bit more controls into its OS. Right now, I'd argue iOS7 in many aspects has more out of the box options and checkboxes for the user to play with.