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.
Mohamed Abdul Rahman was charged with terrorism for participating in a foreign war.
The 22-year-old man was stabbed in the head.
The arrests were made in connection with the rape of a 16-year-old girl in Malé last month.
The seven defendants pleaded not guilty at Thursday's pre-trial hearing.
Judge Adam Arif reprimanded the authorities for glaring failures in the investigation and prosecution.
The government says it is not responsible for his disappearance.
Defence lawyers argued the murder charges were unclear.
The house belongs to the family of a fugitive wanted in connection with a graft scandal.
