I am not sure if you can truncate through the extbase persistence layer. If you want to make your life easy, just use the normal TYPO3 CMS database class:
$GLOBALS['TYPO3_DB']->exec_TRUNCATEquery('table');
Keep in mind that extbase might not know about this truncate and that it might still have some objects in the cache.
The API way would be to call $repository->removeAll()
.