Akecheta's journey into the sub-basement did occur relatively early in the life of Westworld and the repair tech mentioned that they were understaffed. So one could make a leap to think that there were not many security protocols in place and when the employees went to lunch, there wasn't anyone around during that time. However, unlike all the other woke hosts, he did seem unusually calm about being in a totally foreign environment in the sub-basement.
Although I can't give concrete examples, but Akechata and the Ghost Nation seems to have a protective nature towards humans. Akecheta did provide comfort to a delirious Logan. Trying to take Lee away from Maeve's gang when there were going into Shogun World. When Stubbs was captured, he returned to the control center (under a cloud of mystery) unharmed. Emily seems to be aware of this, too. She seemed to know how to find her father and her father was with Akecheta.
How is MIB not dead? Maybe Ford can program the weapons to cause maximum pain to MIB but are still non-lethal. Another FU to MIB... I don't know, I'm reaching on this one.