Yes. There has been at least one color blind pilot astronaut.
“Color Blindness” covers such a wide range of conditions, the term is almost useless. It would be counterproductive to disqualify all astronaut candidates with a detectable color defect. But it would be unwise not to accurately assess for significant defects.
At one end of the “Color Blindness” spectrum is a very rare condition called Achromatopsia (complete absence of color receptors in the eye). Those affected not only have no color sensation, but are severely disabled by normal daylight levels of light.
At the other end of the spectrum are Anomalous Trichromats (one or more color pigments with anomalous absorption spectra). They may be unaware they have abnormal color vision but the deficiency can be detected with specialized testing.
In-between are Dichromats who have two color pigments instead of the normal three. They may be unaware of their color vision deficiency and usually manage well using other clues. For instance, traffic lights are always arranged with the red light on top, a feature which many normally-sighted drivers have never consciously noted. If these people are presented with a colored light in the absence of other clues (such as a red or green navigation light), they may have significant difficulties.
Since there is no one-size-fits-all definition for “color blindness”, astronaut candidates should be tested for the level of color vision performance required for the specific job, as we do for visual acuity. Aviation pilots, mariners and railway engineers need to correctly identify the color of small, dim lights at distance. The appropriate test for this is Farnsworth Lantern Test. The familiar Ishihara Plate Test (which presents numbers made up of dots), works well for screening since most people are familiar with the appearance. Detailed testing for subtle defects requires a Farnsworth-100 test or Anomaloscope or computerized equivalents.
Daniel Brandenstein was Chief of the Astronaut Office 1987-92. He flew 4 space flights, including flights as a pilot astronaut. He failed the Farsworth in 1987. According to http://www.sotos.com/writings/deutan_mission_specialists.pdf he was “severely color deficient”, a fact that was widely known and the source of jokes in the Astronaut's Office. Other astronauts presented him with a black and white photograph titled "The World as Dan Sees It".
So, to answer the title question, yes, there can be colorblind astronauts.