Alternate methods could include adding a MUX or analog switches in the driven interface lines. The programmer would connect on the SPI flash side of the series resistors. The simplest way to do this is to put series resistors in the MCU driven lines between the MCU and the SPI Flash.

The main strategy for the design is to find a simple way to isolate the SPI interface drivers in your MCU system so that they do not interfere with the drivers in the SPI programming pod. DediProg has application information bulletins available to help with correct design for in circuit use. They even sell an adapter clip that can attach into the SOW-16 package without having to design in a separate programming header on your board. This USB connected device can program in circuit if you design your board correctly. One choice is the programmer from DediProg. This also known as in-system-programming (ISP). If you are simply looking for a way to program the Winbond SPI flash with 'pre-loaded' data that your microcontroller would read for use when it is running then what you will want to look into is a programmer that can do in-circuit programming of the SPI Flash chip.