I've implemented Codeception (http://codeception.com) Phalcon1 module to handle functional and unit tests with DB cleanup ability including MySQL. It still in alpha stage though, but should satisfy most common needs.
The only requirement is to create application bootstrap file returning configured DI\Injectable object (MVC\Application for ex). It must not call handle() method, just configure. This file then can be used both in tests and application itself (just include it in index.php to get Application object and call handle()). Hope it will be helpful for some one, Codeception is awesome tool (so as Phalcon ;-)).