I think your problem may not be with JSON.stringify. In the case of exec, it's used to address escaping issues and code-injection when the temporary JS file is written. In your example:

exec('foo --id 909845429478596609')

ends up in the temporary JS file as:

var childProcess = child.exec("foo --id 909845429478596609", {}, function(err) {
    // ...
});

In other words, the individual parts of the command are not stringified, the whole command is. To illustrate how this prevents escaping and code-injection issues, take for example this command:

exec('echo"); console.log("vulnerable"); console.log("')

which ends up as:

var childProcess = child.exec("echo\"); console.log(\"vulnerable\"); console.log(\"", {}, function(err) {
    // ...
});

Without JSON.stringify, it might end up like this:

var childProcess = child.exec("echo"); console.log("vulnerable"); console.log("", {}, function(err) {
    // ...
});

Anyways, this was a long way of saying that the issue is probably with how foo is handling command-line arguments.

@evcohen what happens if you try child_process.execSync('foo --id 909845429478596609')? Success or failure?

We'll remove most uses of JSON.stringify() as part of #782. Therefore, closing this.

I suspect @freitagbr is right, the issue with foo is that it doesn't handle CLI arguments correctly.