Is there anything speaking against just rendering a single point on top of the other stuff?
So just render a single GL_POINTS
primitive at the given pixel. Either use an appropriate orthographic projection to specify the vertex position directly in window space, or just compute the clip space position of the pixel and use an identity vertex transformation. And then all that you need is a simple passthrough fragment shader writing your color of choice.
While you say you want "nothing behind the fragment", I still think that single fragment rendered under the red mark doesn't hurt anyone, at least not more (rather less) than your branch inside the fragment shader just for a single pixel (or any other more elaborate technique using the stencil buffer). If you have any other more strict reason why you cannot render anything else at that position except for the mark, you might want to clarify your problem a bit more.