I've fiddle around a bit. Maybe DeprecationErrorHandler.php:57 is missing a test for DeprecationErrorHandler::MODE_DISABLED?
At first glance it seems to fix the problem, but I'm not sure about possible side effects.

"disabled" mode is taken into account in https://github.com/symfony/symfony/blob/master/src/Symfony/Bridge/PhpUnit/bootstrap.php#L38 - as you can see, this comes earlier than reading the phpunit.xml file.
We could actually change https://github.com/symfony/symfony/blob/master/src/Symfony/Bridge/PhpUnit/DeprecationErrorHandler.php#L105 and read $_ENV['SYMFONY_DEPRECATIONS_HELPER'] there also.
Would you like to submit a PR doing so?

Actually, getenv('SYMFONY_DEPRECATIONS_HELPER') in https://github.com/symfony/symfony/blob/master/src/Symfony/Bridge/PhpUnit/bootstrap.php#L38 will only report environment variables from the shell at that moment. Parameters from phpunit.xml are probably not parsed yet?

As far as I understand the code - and I might be completely off on this - the problem is, that in https://github.com/symfony/symfony/blob/master/src/Symfony/Bridge/PhpUnit/DeprecationErrorHandler.php#L104 the mode parameter is reset to 0 because of https://github.com/symfony/symfony/blob/master/src/Symfony/Bridge/PhpUnit/DeprecationErrorHandler.php#L57 not recognizing "disabled" as a valid value for mode, trying to parse an integer, fails and falls back to 0.

In consequence mode will never be set to "disabled" in https://github.com/symfony/symfony/blob/master/src/Symfony/Bridge/PhpUnit/DeprecationErrorHandler.php#L105.

That's why I used $_ENV in my previous comment. Did you try using it?