One of the problems of the Prusa i3, as you've correctly identified, is that there is an upward force applied to the extruder when it pulls down on the filament. If you push down on the extruder with your finger you can see it move due to the unavoidable flexibility of some of the parts that make up the X and Z axes. All this means that you can get some flexing and unwanted movement of the nozzle whilst extruding, and especially if you have retraction turned on.

The easiest way to deal with this is to transfer the force from the extruder to something more rigid, such as the frame. all you need to do is to get hold of a length of bowden tube, fix one end to the frame with a cable tie and let the other float free. Make sure it's long enough to get from the frame to the end of the extruder in one loop and feed filament through it. The tugging force from the spool is transferred to the frame, instead of the extruder, and you've solved your problem.