with your code, consider the following example:
- texture2D = (1,0,0,1) = red - fully opaque
- colorVarying = (0,1,0,0.5) = green - half transparent
then gl_FragColor would be (0,0,0,0.5) black - half transparent.
Generally, you can use mix to interpolate values, but if I understood your problem then its even easier.
Basically, you only want the alpha channel from your texture and apply it to another color, right? then you could do this:
gl_FragColor = vec4(colorVarying.rgb, texture2D(Sampler, gl_PointCoord).a)