Given that you really don’t care about the absolute dimensions, you can generate a positive mold from a height map image and avoid the entire solid modeling process. Having already solved the cookie press problem, this was a quick-and-easy feasibility study…
Start by selecting the logo, growing the selection by a few pixels, and feathering the edges to produce the mold draft. Then apply a square gradient behind the Squidwrench logo to produce the height map for the edge of the mold. This one is scaled at 3.0 pixel/mm and is 100×100 pixel, thus producing a 33 mm square mold:
One could, of course, produce a non-square mold with a different gradient outline shape.
Hand the image to a slightly modified version of the cookie press script (see below) to get an STL file of the mold:

Feed the STL into Slic3r, hand the G-Code to Pronterface, fire the M2!, and you get a positive mold that looks enough like black chocolate to seem ready-to-eat:

I have no idea whether that will work as a mold, but I suspect flexy silicone putty won’t reproduce much of the fine plastic filament detail, so the negative mold won’t grab the chocolate. The logo is six threads deep with a little bit of draft, if that makes any difference.
The backing plate is 1 mm thick and the height map is 5 mm stacked atop that. A few iterations suggested using about 0.75 gray for the logo; working backwards says 5 mm = 25 layers @ 0.20 mm/layer, so a depth of 0.25 * 25 is about six threads.
For production use, I’d be tempted to import maybe a dozen copies of the STL into OpenSCAD, mount them on a platform with a gutter and a lip on the outside, and then print the whole positive multi-cavity mold in one shot.
The Bash script that produces the mold strongly resembles my cookie cutter script and contains about as much cruft as you’d expect. Because we need a positive mold, not a negative press, the script doesn’t invert the colors or flop the image left-to-right, nor does it generate the cookie cutter STL around the outside of the press:
#!/bin/bash DotsPerMM=3.0 MapHeight=7 ImageName="${1%%.*}" rm ${ImageName}_* ${ImageName}-press.stl ${ImageName}-cutter.stl echo Normalize and prepare grayscale image... convert $1 -type Grayscale -depth 8 -auto-level -trim +repage -flip +set comment ${ImageName}_prep.png echo Create PGM files... convert ${ImageName}_prep.png -compress none ${ImageName}_map.pgm convert ${ImageName}_prep.png -white-threshold 1 -compress none ${ImageName}_plate.pgm echo Create height map data files... ImageX=`identify -format '%[fx:w]' ${ImageName}_map.pgm` ImageY=`identify -format '%[fx:h]' ${ImageName}_map.pgm` echo Width: ${ImageX} x Height: ${ImageY} cat ${ImageName}_map.pgm | tr -s ' \012' '\012' | tail -n +5 | column -x -c $((8*$ImageX)) > ${ImageName}_map.dat cat ${ImageName}_plate.pgm | tr -s ' \012' '\012' | tail -n +5 | column -x -c $((8*$ImageX)) > ${ImageName}_plate.dat echo Create cookie press... time openscad -D BuildPress=true \ -D fnPlate=\"${ImageName}_plate.dat\" \ -D fnMap=\"${ImageName}_map.dat\" -D Height=$MapHeight \ -D ImageX=$ImageX -D ImageY=$ImageY -D DotsPerMM=$DotsPerMM \ -o ${ImageName}-press.stl Cookie\ Cutter.scad
The OpenSCAD program are unchanged from the cookie cutter process.