What makes you think the pirates are raping anyone?
I don't know about raping but we're told that Avery has killed 1000 people, which is 999 more than the Silence but that's OK because he's got a son he has to work out some "issues" with, apparently.
Which reminds me, the pirate says Avery's killed "1000 innocent people." Exact quote.
Now keeping in line with the rule that villains aren't supposed to think of themselves as villains, shouldn't that mean that from the pirates' perspective, they wouldn't consider anyone they kill to be innocent. They'd feel there were legitimate reasons to kill those people.
No one goes around saying "I kill innocent people" unless they want people to think they're psychotic.
Actually, the exact quote was, "I've seen your father gun down a thousand innocent men." Perhaps the pirate exaggerated Avery's actions to disabuse Toby of any notion that his father was a man of honor. Economist Peter Leeson said of piracy,
Even in their time, pirates regularly received pardons for their crimes, and I don't think any of them had a reputation for killing 1,000 innocent people. And really ... "gun down a thousand innocent men"? With a flint-lock?! Maybe firing against other ships with cannons, in which case the count would be rather unofficial, and most likely would have been done with English approval as an "independent" combatant.We normally think about pirates as sort of blood-lusting, that they want to slash somebody to pieces. [It's probably more likely that] a pirate, just like a normal person, would probably rather not have killed someone, but pirates knew that if that person resisted them and they didn't do something about it, their reputation and thus their brand name would be impaired. So you can imagine a pirate rather reluctantly engaging in this behavior as a way of preserving that reputation.
And let's not forget the Doctor himself stole his TARDIS and isn't exactly a law-and-order kind of guy.