I have seen in the development forum that some developers want to have cells only in nine different colours: three shades of blue, three of green, two of red, and one orange. This is because it is thought that this will maintain a more "microbial" atmosphere, as, apparently , neither pinks nor bright yellows are found in microbe microscope images. Yet I have easily found pink and yellow microbe images:
This is due to the fact that, in reality, most microbes are just transparents. Some exceptions are photosynthesizers and other specialized cells with pygments. So the colour of the microbes we see under the microscope relays heavily on the staining of the preparation. Depending of the staining, you can have microbes of all the colours of the rainbow. So, it wouldn't break the microscopic atmosphere to have cells of all colours.
But even more important than that, there are gameplay reasons to have the player choose whatever colour they want for their cells. The frustration at not being able to do so would counter any advantage on the atmosphere. Also it would be easier to differentiate between different species of microbes.
So, I think you should be able to have a full colour wheel for the cell, both for realism and gameplay reasons.