The Miyanos died in a fire that occured in their research lab between 17-18 years ago. Could it be possible that maybe Tsutomu got too close at them during the Haneda Kohji's murder case, and the organization decided to get rid of the couple and started the fire? They often use fire to get rid of evidence. And if Mary really was Elena's sister, then it's possible that the organization thought it was too big a risk to let Haibara's parents live.