First, let me say that the US Navy is currently authorized to harm or even kill orcas and other marine species in the  course of their exercises. Not to kill them on purpose, but allowing them to continue dropping depth charges if a pod of whales come by, that sort of thing. The US government calls any animals killed in this manner "incidental takes."

Now, the incidents you're referring to were the unfortunate result of ignorance during the era. In the 1950s, because marine biologists had not yet made a detailed assessment of orca behavior, the contemporaneous  knowledge of said behavior relied on fishermen's tales. 

Essentially, at the time It was thought that orcas were rage-fueled killing machines who would immediately attack and rip to shreds any living creature they could detect.  In a letter, a 19th-century whaler called them, "a swarm of angry hornets boiling through the seas, only satisfied by the agonies of suffering."

 By extension, it was believed that they would try to sink any ship that strayed too near to them, and that they would relentlessly attack until they succeeded or died.  In fact, the conventional wisdom was even that sinking boats was the activity orcas most cherished, and that any boat under 30 feet should immediately sail for shore.

This may sound a bit comical, but it was a deadly serious belief at the rime. Icelandic fishermen truly were apt to flee in terror if orcas were spotted.

You can probably see where this is going. Due to their reputation, the US Air Force used them for target practice on strafing runs. They and the Navy dropped depth charges on them. In the minds of military personnel, they were killing two birds with one stone: maintain readiness and eliminate a threat. This happened for a decade-plus, as late as 1964.

The worst incidents that  we know of were indeed because fishermen in Reykjavík often complained that a large contingent of whales were ripping up their fishing nets. We don't know how many orcas, exactly, that the US Navy slaughtered in an effort to aid fishing operations, but several sources report it simply as "thousands."

Today, the concept of an "evil" species sounds like childish ignorance. Because it is. And it was. The ignorance of all humans involved led to an entire population being senselessly slaughtered.

ESIT: I should note that this answer relies partially on the memoir When Devil Fish Come Out to Play, by retired diver and former special assistant to the Canadian Minister of National Defence, Calvin Smith.