'Footprint Field' visibility options in Eeschema (Kicad)
I don't know the direct method, but you can manually modify the text file *.sch (remember to backup before modifying).
For every component, there is a record in .sch file, and the footprint field is normally field number 2, e.g:

 $Comp
  ...
  F 2 "Name" V 10000 2500 50  0000 C CNN
  ...
 $EndComp


the value of 0000 near the end indicates that this field is "visible", and you need to change this to 0001 ("invisible")

How? by regular expression.
I used the following command in vim:

:%s/^F 2\(.*\)0000 C CNN$/F 2\10001 C CNN/


you can try sed or any kind of text-processing app to do it.

Source:
http://en.wikibooks.org/wiki/Kicad/file_formats#Description_of_a_component