I cant say that I completly under stand your question. 12mp will allways have 2x the data as 6mp.
Yes Software may be able to smooth out the lines, and avoid pixelation, but that does not increase the ammount of detail in the shot. So the interpolated image will still only have half as much detail as an image that started off at 12mp.
An example of detail. Take a picture where a fish shows up as 100 pixels. You will be able to see the shape of the body and where the fins are, but the details of the fish such as scales will not be visable. You can interpolate that fish to 200 or 400 pixels but no ammout of software processing can make scales show up on that fish. But if your camera had higher resolution, the fish would take up more pixels from the start, and the scales might be visable.
Clearly for small prints, the extra detail will not show up so there is no point to haveing more mp. Prints are usually done at 300DPI so up to a 10"x6" there will be no difference between a 6 and 12mp camera. But any print bigger than that, the 12mp image will contain more detail, at least if you look close enough.
The point where a person picks up on the extra detail depends on the person, and the viewing distance. If you never print bigger than an 8x10 or you dont look at your 16x20 from 6 inches away, you may never see the difference.
But eventually as increas print size (or decrease viewing distance) you will notice the lack of detail and at what ever size that is, you would be able print a 12mp one twice as big.(in terms of area) before you noticed it.
Is the extra deatil worth spending $3000? That one is up to you.