working illegally and not saying anything isn't exactly a recommendation for hiring someone.........employers hiring illegals can have their own work-permit and visa cancelled for breaching the law.........and ignorance is no excuse.
there's an MOU between Thailand & Myanmar enabling the workers easy access to affordable work-permits and visas. The Agency can't issue a work permit for her, if they do that she becomes their employee. If you need help making her legal she should know an agent to do it for her..........I'd ditch her tbh if she's been working illegally and the agency never said anything. Ditch them too.
Myanmar citizens appying for ED visa will be booked into a proper school........or Uni. They dont need to cheat the system, there is an MOU betwenn Thailand & Myanmar allowing work-permits and visas to be acquired cheaply and with minimal fuss. Laos and Cambodia too.
being in possession of a visa does not guarantee you access to anywhere. It isn't implied anywhere that entry is guaranteed either. This is the case for every country and is internationally accepted practice. The Immigration departments around the world can and do refuse entry to people. It isn't a decision they make lightly and so it isn't something that occurs regularly but they have to have that power/option to stop undesirables.