"done what 3dRealms would have done with that 6 million."
What 3D Realms claimed, and would have liked Take-Two to believe, that they would have done. Something they claimed they were on the verge of achieving for a decade, and which never came to fruition. What makes you believe they would have accomplished in that final year what they had failed to accomplish for the past decade? What makes you believe they would not simply have started over again?
I find it questionable that 3D Realms would ever have released DNF on their own. I think they would have burned through that money and still not have had a finalized product to show for it, as they seem to have been doing for quite a while, which is probably why the publisher declined to give them the money.