The 20-year-old was attacked by five men in Maafannu.
A very capable team worked on the investigation, the ex-police chief said.
The Bangladeshi embassy was unavailable for comment.
One of the cancelled trials was for ex-president Maumoon Abdul Gayoom.
Aishath Fazna told local media she was resigning for personal reasons.
Naseer believes the president thought too many state resources were being used.
Three-year-old Ibthihaal Mohamed was found dead at his home in Vaavu Rakeedhoo island in 2015.
New rules on criminal trials came into effect on Wednesday.
Police knew Rilwan was followed by a suspect who was allowed to leave the country.
Haris Abdul Gafoor was stabbed to death last year.
The man was stabbed eight times on Tuesday morning.
The court did not give a reason for throwing the charges out.
The president denied thwarting the investigation into the missing journalist, "who is now dead."
It is almost four years since Ahmed Rilwan disappeared.
Ibrahim Rasheed was severely beaten during a police crackdown on February 8, 2012.