Chris Taylor, who is the Executive Director of the Atchison County historical museum, which is situated at the old freight depot in Atchison, called me just a few minutes ago and with some answers--The last intercity passenger service though Atchison ended in 1960 or 1961--it was operated by the MoPac RR, (a contraction of Misouri Pacific)--He says that at that time, it would have been necessary to make a connection to get to Santa Fe, probably at Oklahoma City--
He said that at that time, there were also commuter cars called doodlebugs, which ran to Topeka, and that those went out of service without much fanfare a few years later(the interstate highway system was built during the late 1950's, and after that, the automobile became the preferred means of transit)--
As to ATSF line, which now only runs out of Atchison a few miles west to Parnell, he says that the main line to Topeka was abandoned in 1994, but with a stipulation that the track be sold to an organization that would preserve it for excursions--according to him, the organization that did acquire it "Pulled a fast one" and tore up the track, selling it for scrap, and ending the great rail line forever--
If you, or anyone, has questions for Chris, he can be contacted at Atchison.org. He's a nice guy--