The error probably means that you have selected a wrong configuration.
To modify the IDE to insert the -F seems to be the hard way,
however the easy way is to make a wrapper to avrdude:
$ cd ./arduino/hardware/tools/
$ mv avrdude avrdude.orig
$ cat >avrdude.sh
#!/bin/sh
./avrdude.orig -F $@
^D
$ chmod +x avrdude.sh
$ ln -s avrdude.sh avrdude