The MSM/liberal view is that the EPA are the good guys no matter what. In their view, it would be better to shut down as many mines as possible to pre-emptively halt damage, and the EPA is useful for that.
As for government bureaucracy and incompetence, that doesn't register with them either. Liberal statists believe bigger government is better government, and some inefficiencies must be tolerated. Besides, big stupid government is union friendly, and liberals like that too. As icing on that cake, everyone knows that a government job is a secure job.
Over eight billion budget and seventeen thousand employees so they need to justify their existence.