Ok, I have found a way to do this:
Load all the Ekos produced FITS files into the "Conversion" tab of Siril
Use the "Convert" button, with the "Debayer" box checked to create new FITS files that have R,G, and B channels.
This method changes the FITS header from:

BITPIX = 16 / number of bits per data pixel
NAXIS = 2 / number of data axes
NAXIS1 = 4144 / length of data axis 1
NAXIS2 = 2822 / length of data axis 2

to:

SIMPLE = T / file does conform to FITS standard
BITPIX = 16 / number of bits per data pixel
NAXIS = 3 / number of data axes
NAXIS1 = 4144 / length of data axis 1
NAXIS2 = 2822 / length of data axis 2
NAXIS3 = 3 / length of z axis (mostly colors)

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