MSeifert February 2016
The only way I could think of is just pass in the data-array instead of the fits file. If it has no WCS information it must operate in pixel-space.
from astropy.io import fits # or import pyfits
with fits.open(filename) as hdus:
data = hdus.data
f1 = aplpy.FITSFigure(data)
# ... whatever you want to do thereafter.
I haven't used APLpy maybe there is a better way but I haven't found anything in the documentation.