Certainly counterproductive from the standpoint of the central Government: the individuals being killed are not significant players, and pose no real threat. The Government loses far more in the public relations battle that it gains in the fight against insurgency from these incidents.
It's important to remember, though, that political violence in the Philippines is overwhelmingly local and very frequently personal. We often hear about the numbers killed during elections and campaigns, what we hear less often is that it is not national campaigns that spur violence, but contests over local offices. This is where the old family feuds and personal vendettas come into play.
In many of these cases there are direct personal conflicts involved: "militants", generally on the left, often come into direct conflict with local leaders and military commanders. Many of these people are thin-skinned and do not take well to accusations and perceived insults. They are also effectively above the law.
The NPA also survives in most areas through "revolutionary taxes", which essentially amount to extortion. This process often runs up against local economic interests, which generally overlap closely with political power. In some cases local political and military figures are running very similar protection rackets, and when the rackets rub up against each other violence often ensuers. One response is violence directed at those known to be NPA allies, who are often easier targets than their comrades in the mountains.
It is also completely true that many of these "militant" groups are closely allied with the NPA and that in many cases their memberships overlap. This is, as stated above, a reason for the general lack of public concern. A common "man on the street" reaction would be "kasama 'yan sa laro"... literally, "that's part of the game", though a more accurate equivalent might be the old aphorism "if you can't take the heat, stay out of the kitchen".
I very much doubt that the killings are directed by the central Government, but the Government does not have the will or the capacity to stop them.
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