I remember something similar at LAUPT when I was down in November. They were doing some work at the terminal (adding another lead, if I remember correctly), and Metrolink and Amtrak trains were significantly delayed because only one movement was allowed in or out of the terminal at a time.

There were "trained Metrolink switchmen" (according to the Metrolink press release--in other words, conductors and/or brakemen, if Metrolink has them) manning the switches as CTC was disabled during the trackwork and for a test period after the work was finished (they needed to test the 220 different combinations of routes, each test requiring an hour, probably to manually inspect the switch points to ensure they were lined correctly).

My guess is that the UP had "trained UP switchmen" at Binney. They'd have to be a craft authorized to throw switches, and I'm not sure that MOW workers (or even foremen) can be authorized by a dispatcher to throw switches for trains (although I've had them line trains into and out of sidings with the conductor's permission).