Most people don't think their stance is ever political. But it very clearly is here since Twitter would be directly at odds with the Pakistani government if they sided with the journalist.

From his description, he only suspect the government to be behind the troll accounts. So by blocking/fact checking the trolls Twitter wouldn't take any risk it seems. It seems more likely they are unable to understand or verify the messages of the trolls.

I agree—if only it were that clear and simple.

It is simple in many cases that are currently allowed on Twitter. They aren't making a good faith effort to solve the issue. Evidence: Allowing quote tweets directed to users who disabled replies. This is always used as a vector of further harassment.