The bottom line here is that the Philippine government is losing...

The bottom line here is that the Philippine government is losing significant taxation from the lack of action. They would appear to be making the company suffer through lack of communication.
If there is so much hostility to the mining licence being granted then one would have to consider that the company has been a little less forthright in its responsibilities towards the environment.
So one could think that the licence could be granted with heavy penalties for environmental damage if it can be proven that it was the company and not a "false flag" by the protesters to try and frame the company. Obviously also with strict monitoring.
At some point something will have to give.