Science or Prejudice?

In surfing the net earlier, I discovered a fascinating article on the Esmerelda, the earliest known ship from the Age Of Discovery. She was part of Vasco da Gama's Indian Armada, ordered by King Dom Manuel, in 1502, and was under the command of his uncle, Vicente Sodré. She sank in May, 1503 off the coast of Oman and was discovered in 1998.

In the depths of the article, this little throw away occurred,

Ancient weaponry, including firearms, was also found and provides proof that Manuel ordered military objectives from this fleet, which were carried out "brutally" according to the archaeologists.

My question is, how exactly do these 'archaeologists' know that the military objectives were carried out "brutally"? Did Dom Vasco da Gama leave a log that recorded, 'Oh, by the way, I carried out Dom Manuel's military objectives brutally'?

Or did the 'victims' of this 'brutality' leave records that said, 'In 1503, we were the victims of brutally carried out military objectives by the Portuguese.'?

Or, is this a survival of La leyenda negra transferred to the Portuguese as A lenda negra? For those not familiar with the 'Black Legend', it was (is?) an anti-Catholic school of historical writing which strives to pain the Spanish Empire in the darkest colours possible. It presents Spain and her Empire as cruel, bigoted, exploitative and self-righteous. 

I wonder if these 'archaeologists' have decided that since Portugal and its Empire were Catholic as well, it also must have been cruel, bigoted, exploitative and self-righteous?