main.php

<?php

if (extension_loaded('xdebug')) {
	// Use a empty php.ini and not extra ini files
	putenv('PHP_INI_SCAN_DIR=/tmp/composer-php-empty');
	passthru('php -c php.ini main.php', $exitCode);
} else {
	// Run with the env var
	passthru('php sub.php', $exitCode);

	// Reset the env var
	putenv('PHP_INI_SCAN_DIR');
	passthru('php sub.php', $exitCode);
}

exit($exitCode);

php.ini

; Empty

sub.php

<?php

var_dump(extension_loaded('intl'));
var_dump(extension_loaded('xdebug'));

Outputs:

bool(false)
bool(false)

/Users/renan/test/sub.php:3:
bool(true)
/Users/renan/test/sub.php:4:
bool(true)