Some possibilities:
Use the image function along with contour or contourlines to do your own (approximate) version of filled.contour
Extract the code from filled.contour to just make the plot without the separate frames and legend
use the levelplot function from the lattice package (arrange multiple plots using either grid or print.trellis)
See the ante-penultimate example on the help page for stat_contour (ggplot2 package as requested, you will need grid to arrange multiple plots)
Make separate plots using filled.contour, send to files, then add the multiple plots to an empty plot using rasterimage, or better use a tool like imagemagick to combine the files.