I had considered the Defender because of the holster, but I read that the holster isn't that great and secondly I think the Defender is just way too thick.
FWIW, I hardly ever use the S-Pen, but I have tested it and have not noticed any ill effects from the magnet. I believe any issues may just be an issue of perception (if you go looking for the problem you will find it). It's not like the magnet causes the S-Pen to malfunction and causes mystery text to appear like a Ouija board. I've covered the screen from top to bottom with squiggly lines and do not notice any difference between the area where the magnet is located, and the rest of the screen.
Looking at the Surface case, I don't see how you would be able to remove the magnet without damaging the case itself. You would have to pry out the kickstand since the magnet is located behind the kickstand housing. Besides, without the magnet in place, the kickstand would swing loosely.