The original scheme devised by The Department Of Transport in the good old days before we had TfL inflicted upon us did involve grade separation of the three main flows of traffic.
The A1 was to go underneath in a tunnel, the A406 was to retain its current course and above, as at Brent Cross, there was to be an elevated roundabout into which the A598 would feed directly. It was in preparation for this scheme that Henly's Garage was moved and the land acquired.
I think you underestimate TfL's determination to prevent real improvements from ever taking place. It wasn't that they allowed themselves to be influenced by a few nay-sayers. They actively sought them out in order to have a pretext for their wasteful scheme. This is standard practice by unscrupulous public bodies.
On any subject under the sun there is always a handful of cranks with a perverse opinion. If a public body wants to do something that the vast majority of people oppose, the trick is to seek out the cranks, ne'er-do-wells and utterly selfish people who don't give a damn for the public interest and then claim that these people represent the majority.