Comment 8 for bug 1342677

I guess you can patch as you wish for the upcoming release on Ubuntu.

But for longer term, how about updating debian/rules as:
(Just give me the line for NotShown.)

override_dh_install:
        dh_install
        # Adjust priority for each distribution.
        # Debian: ibus (21) fcitx(22)
        # Ubuntu: fcitx(20) ibus (21)
        if dpkg-vendor --is ubuntu; then \
                cd debian/im-config/usr/share/im-config/data ; \
                mv 22_fcitx.conf 20_fcitx.conf ; \
                mv 22_fcitx.rc 20_fcitx.rc ; \
                echo "NotShowIn=MATE;GNOME" debian/im-config/usr/share/applications/im-config.desktop ;\
        fi