Assuming that you are building from the Yocto complete image: http://downloadmirror.intel.com/24698/eng/edison-image-ww05-15.zip
The easiest way to do it would be to edit /path/to/edison-src/build/conf/bblayers.conf and delete the one line with the word arduino.
BBLAYERS ?= " \
In effect, this removes a single package called clloader from the image.
as described in other threads within this forum (e.g. Re: Can the Arduino emulation mode be disabled?): there is not much magic around running Arduino sketches on Edison as they are just standard Linux processes. You just need to disable the clloader service (see link) and you should be fine.