Would it be unlikely for CDOT to step in and take over the new haven, similarly to the MTA and NJT?To answer your specific question: The ONLY reason the government approved the merger of the PRR and NYC was because it was seen as the ONLY way to save the New Haven, which was hopelessly bankrupt and unwanted by everyone but which was vital as a New York-Boston carrier. Any scenario where the PC merger is avoided thus has to come up with some means of addressing the fate of the New Haven; probably the only alternative would be nationalization as an early form of Amtrak or Conrail.
Most everyone in the 1960s expected the PRR to line up with the emerging N&W system and the NYC with the C&O-B&O. That of course is how it eventually shook out anyway, when CSX and Norfolk Southern split up Conrail. Find an answer to the New Haven, and you might well have seen everything coalesce around competing PRR- and NYC-based systems.
Would it be unlikely for CDOT to step in and take over the new haven, similarly to the MTA and NJT?
Given the political realities of the 1960s it would be very hard to convince enough people that nationalization at the state or federal level is a good idea. Railroads were still thought of as cash cows for tax revenue at the time. And they deeply resisted any form of subsidy, because they feared it was a foot in the door to nationalization. They didn't want subsidies; what they wanted was for the government to STOP paying for highways and airports (which, of course, wasn't going to happen). You really pretty much need a disaster of Penn Central-like proportions to create enough disarray to make nationalization palatable. Maybe if the New Haven, like PC around 1972-73, threatens to shut down completely.