Well, your under-exposure experience is interesting. I have had the D7000 since last October and encountered no difficulties at all, in any exposure mode. I am, however, in the habit of intervening manually if I think a scene warrants it as I never fully trust automated systems. For careful work I always use the histogram and make adjustments accordingly.
I live near the Rocky Mountains and do some photography up there. Scenes are typically extremely contrasty (glaring white snow and deep forest shadows). With both the D300 and D7000 I sometimes end up under-exposing (in relation to what is recommended by matrix or weighted readings) by as much as 2 full F-stops. This saves the highlights and I can still pull out plenty of detail in the shadows *without problems from noise*. I have never found it necessary to use noise abatement software with either camera. The D7000 has a useful 9+ EV's dynamic range which is excellent. Relevant to your situation, perhaps, is the fact the D7000 proves significantly better at this "expose for the highlights, develop for the shadows" approach than the D300, although the latter is no slouch and a great standard in its own right.
It's a bit puzzling that in your case some underexposure leads to unacceptable noise performance in a camera which sets a new standard in this regard, at least for APS-C format. If you could find someone handy to compare D7000 results that might help determine if your unit has a defect. It happens. That might be the best approach to making progress with your concerns.