When Cibo and Killy enter the elevator for a ride the first time, Cibo is very suspicious about the elevator man.
Which is no wonder because he/it is indeed very strange, all rotten and stuttering.
But the ride is safe.

When Killy finds himself placed in the elevator by Dhomo to bring him outside of the unofficial megastructure he meets the elevator-man again.
This time he/it is transformed into a huge safeguard to stop Killy from trying to change destination of the elevator.

Why was the elevator-man transformed into a safeguard ?
Why wasnt a safeguard downloaded from different matter ?
And with Killy defeating the elevator-man, does this mean the elevator doesnt work anymore ?

The elevator man is just a machine, indipendent from the safeguard and integrated into the system of the megastructure. Think of it as the 'human' robots in Blame!#2. Maybe he becomes aggressive to Killy because of Dhomo's disposition at him.

Didn't the mainframe system try to stop the Safeguard from killing Killy and Cibo several times?

Perhaps it lost control again and wasn't able to keep the Safeguard from taking over the Elevator-Man.

Maybe it's a security-device to prevent the elevator from taking damage and securing further functionality. So the elevator-man sees a thread in Killy and tries to destroy him to safe himself...