I like the agency and all, but boy, aren't they scary
First off, the first thing General Rama decided to do after Ali got his hand on IRIS was to execute him before Bakar (and Jenny) intervened. And even then Ali was considered the agency's, and I quote, "property". That's illegal.
Secondly, while it's not explicitly said, MATA is a child soldiers factory. They're training children to fight their war whether inside Cyberaya or outside.
And third and lastly, by using Protokol Gegas as an excuse, they can abandon those child soldiers who've been nothing but loyal to them just because a mission doesn't go their way. While this is a noble moral code, again I repeat that literal children are expected to carry this code as we've seen during S1E7. Right on the next episode, even General Rama admitted that he was grateful Ali wasn't a good agent and had disobeyed a direct order because he wanted to save Alicia.
Bear in mind that MATA is Cyberaya's military first and foremost, founded and funded by none other than Dato' Othman to protect Cyberaya from threats. They're not created as a justice system like the police is. They're just there for Cyberaya's interest and could care less about people's plight such as the Pinggiran.
...okay, I've cooked enough. Time to sleep