Can't scan a precursor anamoly

I'm not sure if I did a big mistake here or if this is a bug. But dotted all over the maps you have heavily defended precursors anamolies. However, when you attack these, they are classified as pirates. So... I was annoyed by being constantly having my explorers and probes attacked by pirates... So I did the "ally with pirates perk". 

Now... If I attack one precursor anamoly with a force that isn't overwhemingly strong... I won't completly defeat the defenders of the anamoly, and they will now be visable on the map, and I can't send other ships to attack the target, because now they are listed as pirates on the map, whom I'm allied with.