I forgot to mention that this was tested on the mini breakout board, not the Arduino board. The Arduino board has other logic in the way, so you would not see any changes in the internal pullups on that board.
even easier: use libmraa which is already included on Edison Yocto (but you should upgrade to latest version as described elsewhere in this forum).
libmraa abstracts the hw details so you don't have to deal with sysfs
It supports C/C++ and has even Python and Node.JS bindings
How do you change the pullup strength in libmraa?
I checked - it's indeed currently not supported by mraa. Sorry