Why didn't Kira kill manipulate the mafia to kill Mello? In the Mafia Arc, Kira was able to get hold of the names of the Mafia members under Mello's command, but the only thing he did was kill them. Couldn't he have manipulated them to help out in the assualt/kill Mello themselves?

Seems like a plot hole to me.

The same could be said for Mello killing the majority of the SPK members - he could have manipulated them to kill Near. However, this could be forgiven because he might have wanted to 'fight' Near 'mentally' with defeating Kira, the last boss.

Is there a rule that prevents them from manipulating to kill?
There is a rule indicating that someone's death must not cause another's:


  Whether the cause of the individual’s death is either a suicide or
  accident. If the death leads to the death of more than the intended,
  the person will simply die of a heart attack. This is to ensure that
  other lives are not influenced.


From http://deathnote.wikia.com/wiki/Rules_of_the_Death_Note