Given the threat that Krall and his represented to the Yorktown Space Station, it seems like they could have done more to kill him.
Scotty was already working with their operations people at the time so there was not a problem communicating his presence and that he was a threat.
It seems like somebody could have beamed him into a holding cell, or into outer space, or just spread his atoms around the solar system.
They also had flying police cars. Why didn't one of these just fly up to him and put a hole in his chest!