This is a good feature to add.  A few requests:

1) Change the environment variable name to match other node config environment variable names, and state it in the positive:  NODE_CONFIG_PERSIST_ON_CHANGE="Y/N" (with the default being "Y")

2) Make the change inside _persistConfigsOnChange(), because it should disable persistence regardless of where it's called (there is another place _persistConfigsOnChange() is called).

3) Document the environment variable usage and default (probably in doc/template/overview.tmpl)

4) Extra bonus points:  Write a test to verify it works, and continues to work through future changes.

My suggestion is to add something like this to the top of _persistConfigsOnChange():
if (process.env['NODE_CONFIG_PERSIST_ON_CHANGE'] === 'N') {
    return;
}