Lou Menk, the 1st Chairman of BN and formerly of Northern Pacific & Burlington, was not a supporter of passenger trains. I have read where he was so tied up in implementing the merger that he had not yet devoted much thought to the road's passenger trains. Perhaps Menk, like other RR bosses, was simply waiting for the Federal government to decide whether to subsidize the nation's remaining passenger trains. If Amtrak had been turned down, I'm sure the bosses ( and the I.C.C. ) would have seen it as a green light to cut the remaining passenger trains.
Regarding repainting equipment, recall that Burlington Northern was very quick to develop an image & paint scheme of their own, having had a 2 year court delay to help provide the necessary time. The new RR quickly removed the NP Monad from locomotives, as well as the GN Billy Goat & SP & S oval logos. Repainting passenger equipment into a unified scheme was a great way to put the new company out in front of the public.