According to Richard Rhodes in The "Making of the Atomic Bomb", Gen. Groves assigned a Major John H. Dudley the task of finding a location for Site Y in October, 1942. He originally picked a location near Oak City, UT but that site would have required the relocation of several dozen families and remove too much farmland from production. The next choice was Jemez Springs, NM but upon inspection, Groves did not like it. Oppenheimer then suggested Los Alamos which had previously been rejected by Dudley since it didn't meet Groves's stated requirements. Groves said ok, 'if it will keep the longhairs happy'. Rhodes also refers to a Corps of Engineers' appraisal prepared on Nov 21, 1942 setting the value of the Los Alamos Ranch School at $440,000. Construction of the barracks & buildings started almost immediately.
Since the organizing & planning conference was held in Apr, 43 (Oppenheimer arrived in Mar, 43) and the project equipment only started arriving shortly thereafter, what would have been the purpose of a "secret railroad" that was scrapped in late 1942? It only makes sense that if it was still there in late 42 Gen. Groves would have kept it going for a while longer.
By the way Ghost Ranch was indeed a dude ranch but it was also an artist's colony (among others, Georgia O'Keefe made her home there). Hardly a high security location to my way of thinking. It's only about 30 miles south of Chama and a long ways from Los Alamos.