I use both the front and rear brake in combination all of the time. The linked braking took some getting used to, but, after 12,000 miles I've become accustomed to it and generally don't notice it much any more.
Pretty much my way as well, and while I notice the pulsing, I just stopped caring about it. I would have loved an "Off" button for the linked system, but that doesn't seem to be in the cards.
I've also noticed that I am becoming Connie-ized and using the foot brake less and less all the time. The computer does a damn fine job of sharing the load with front-braking only, and over time, unconsciously, I have found myself braking to a stop with my right hand only. I still use both when cruising, but mostly out of habit I think. The system keeps the suspension pretty solid.