The choice here is really between an '06 leftover model vs. a new and updated '07 model. That the '06 has a straight six diesel and the '07 a V-6 diesel is secondary to the economics of "new model" vs. "leftover model".
I'd buy the '07 V-6 in an instant but I can't as I live in California where it's not yet sold. Urea exhaust treatment eliminates NOx and may eventually qualify it.
Why do you suppose M-B designed a new diesel, not just for fun, it's a better power unit and will also be offered in the '07 Jeep Grand Cheroke as well. In Europe the V-6 diesel is offered in the E and S class models.
Beyond the diesel engine, the '07 E class model has some improvements over the '06 that one should also consider.