By looking at the source of the spellchecking plugin, we can see it relied on Hunspell dictionaries.

Let's find all the interesting occurrences of hunspell:

~/.atom/.node-gyp/.atom/.apm/spellchecker/0.9.0/package/vendor/hunspell
~/.atom/.node-gyp/.atom/.apm/spellchecker/0.9.0/package/vendor/hunspell_dictionaries
/usr/local/share/atom/resources/app/node_modules/spell-check/node_modules/spellchecker/src/spellchecker_hunspell.cc
/usr/local/share/atom/resources/app/node_modules/spell-check/node_modules/spellchecker/vendor/hunspell_dictionaries

Now, let's find other dictionaries installed: find / 2>/dev/null | grep ".aff$"
You might get interesting stuff in those directories:

/usr/share/hunspell/[LANGUAGE-SPECIFIC].aff
/usr/share/ispell/[LANGUAGE-SPECIFIC].aff
/usr/share/myspell/dicts/[LANGUAGE-SPECIFIC].aff
/opt/libreoffice4.1/share/extensions/dict-[LANGUAGE-SPECIFIC]/[LANGUAGE-SPECIFIC].aff
~/.mozilla/firefox/[RANDOM-STUFF]/extensions/[LANGUAGE-SPECIFIC]@dictionaries.addons.mozilla.org/dictionaries/
~/.config/libreoffice/3/user/extensions/tmp/extensions/[RANDOM-STUFF].tmp_/[LANGUAGE-SPECIFIC-PLUGIN].oxt/dictionaries/

And now, instead of editing /usr/local/share/atom/resources/app/node_modules/spell-check/node_modules/spellchecker/src/spellchecker_hunspell.cc, backup those files :

/usr/local/share/atom/resources/app/node_modules/spell-check/node_modules/spellchecker/vendor/hunspell_dictionaries/en_US.aff
/usr/local/share/atom/resources/app/node_modules/spell-check/node_modules/spellchecker/vendor/hunspell_dictionaries/en_US.dic

And replace them with some other dictionary. I took the following files, renamed in order to overwrite the two above:

/opt/libreoffice4.1/share/extensions/dict-fr/fr.aff
/opt/libreoffice4.1/share/extensions/dict-fr/fr.dic

Initially, I thought that tweaking ~/.atom/.node-gyp/.atom/.apm/spellchecker/0.9.0/package/vendor/hunspell_dictionaries would do the trick, but actually no.

Not perfect, but better than nothing!