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Dornhege's link to the other discussion (ending ultimately with an enhancement request ticket for rviz) is certainly correct.

However to answer the question more specifically: yes you can do this with a Marker. Specify marker type SPHERE, set the marker.scale.x, y, and z values to the length you want each axis of the "sphere" to be. If the scale x, y, and z values are not all equal it will look like an ellipsoid instead of a sphere. Set marker.pose.orientation to give it an orientation and marker.pose.position to the location of the center, and you are all set.

I'm not the one to ask about the math to go from a covariance matrix to a rotated ellipsoid, but I know you can show rotated ellipsoids in rviz.