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
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
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.