As I understand the Condrix were like remote eyeballs for the Murexes to scout out Earth. The plan was to send the Murex so many cursed images that it would freak out and run away (some LD dialogue even suggests the players are mindfucking it into permanent insanity).
To replace the real data with garbage data, the ground teams would beat up the Condrix, steal its security codes to convincingly dress up the garbage data, and then the space team would directly inject them back into the Murex.
The Railjack team would then use those codes to basically ghost hack the Murexes and lobotomize them.
They were likely not very sentient afterwards.
Naia, being partially Sentient, must've felt sorry for the Murexes. I mean, getting slowly lobotomized and losing your mind can't feel good.