Continuing https://stackoverflow.com/a/20574486/4935114, @Mike proposed to create a pre-commit hook which will grep in the staged files for the lines which one might want to ignore. The hook checks if those lines were staged. If so, it echos a warning and it exit's with code 1 so the commit process won't continue.
Inspired by @Mike's answer, I found myself using perhaps an improved version of his hook which automatically resets (with the -p flag) the specific line which we want to ignore.
I'm not sure this hook will work for a situation where you have many files with this line to be ignored, but this pre-commit hook looks for a changed in this line in a specific file buildVars.java. The hook script looked like this when I tested it on my machine.
#!/bin/sh
# this hook looks for lines with the text `var isPhoneGap = false;` in the file `buildVars.java` and it resets these lines to the previous state before staged with `reset -p`
if [[ $(git diff --no-ext-diff --cached buildVars.java | grep --count -e "var\ isPhoneGap[\ ]*=[\ ]*") -ne 0 ]]; then
    cat <<EOW
WARNING: You are attempting to commit changes which are not supposed to be commited according to this \`pre-commit\` hook
This \`pre-commit\` hook will reset all the files containing this line to it's previous state in the last commit.
EOW
    echo /$'\n'isPhoneGap$'\n'y$'\n'q | git reset -p
    # BONUS: Check if after reseting, there is no actual changes to be commited and if so, exit 1 so the commit process will abort.
    if [[ $(git diff --no-ext-diff --cached | wc -l) -eq 0 ]]; then
        echo there are no actual changes to be commited and besides the change to the variable \'isPhoneGap\' so I won\'t commit.
        exit 1
    fi
fi
Explanation
What I did was echoing a control sequences which searches for the regex isPhoneGap during an interactive reset process. Thus emulating a user who presses / to search for isPhoneGap, presses y when asked if he wants to discard this patch and finally presses q to exit the interactive reset.
The interactive reversed patch process is documented here: https://git-scm.com/docs/git-add#git-add-patch
NOTE: The above script assuming that the variable interactive.singleKey is false. If you configured yours to true, remove any $'\n' from the echo command right after the warning.