Earlier quoted context omitted.
All regularization work I'm aware of uses W=I (an identity matrix). Where did you find this zero origin matrix? Note that your W does not guarantee invertability - e.g., if your original (0,0) is already 0.
This was shown by Professor Andrew in the Coursera ML class that's happening right now. Given n features x1 to xn we introduce x0 feature which is always set to 1. During the Regularization lectures the professor said that we don't need to control (or regularize) the theta0 (the parameter for x0) because it doesn't make a difference. I believe this is the reason W(0,0) is set to 0. The lectures are a little light on…
He doesn't need to set W(0,0) to 1 specifically because he sets x0 to 0 (which guarantees a non-zero value in the covariance matrix).
But the standard way to do L2 regularization (also known as "ridge regression") is to add a scaled identity matrix (the entire diagonal set to be nonzero)