How did Itachi awaken his Mangekyou Sharingan? If Itachi didn't kill Shisui, how did he really awaken his Mangekyou Sharingan?
The Mangekyou Sharingan is activated once its user experiences great loss, especially of someone close to him.
This means that Itachi did not have to kill Shisui in order for the Mangekyou to activate. What is most important for the activation is that the user feels the loss, which causes their brain to release a special kind of chakra that affects their optic nerves (chapter 619), thus awakening the Sharingan, and the Mangekyou, depending on what 'level' you were before, and on how much loss you have experienced. The more loss you experience, the more powerful the Sharingan gets.  

Probably, just witnessing Shisui's death to protect the village was traumatic enough for Itachi to awaken his Mangekyou.
Also, if you remember, Sasuke's Mangekyou activated when Itachi died. He did not kill him either, but witnessing his death, even though he hated him, was traumatic enough to activate it.