Sequence of tenses

Hello , please look at the following abstracts. "In addition, the troubling vacuum at the top of Thai society means that no one is setting the tone for the period of mourning now under way. That has allowed a sort of hysteria to develop, in which people seen as insufficiently respectful are accosted by angry mobs. The police, instead of protecting the victims of such attacks, tend to arrest them, and in at least one case forced a suspect to prostrate herself before a picture of the late king. The minister of justice has condoned royalist vigilantism, and the authorities have opened a series of new investigations into supposed incidents of lèse-majesté.

As it was, the army had been using lèse-majesté and other laws to suppress all manner of inconvenient debate, over the incompetence of the ruling junta, say, or shortcomings of the illiberal constitution it foisted on the country earlier this year. The accession of a new king gives the junta an opportunity to ease up, especially as there is little sign that advocates of democracy are seeking to exploit the moment. Instead it seems inclined to restrict freedom of speech even further"
Please tell me what does the past perfect denote in the beginning of the second abstract? The storyline is set in the present so why is past perfect used. And please explain what does "as it was" means. Thanks a lot