Im just gonna throw this out there,just to get people thinking.

What if it was...Rei?She's the last person we would expect.
It would ad to her change near the end of the series.She was completly loyal to gendo and im sure she would do it if he told her to.

If i were gendo i would send Rei.It's not like she would show any outward sign's of being a murderer.

No one would ever suspect her.

How about it was some random SEELE lackey?

ep #21/21' wrote:FUYUTSUKI:
Oh, it's you.

Kaji:
Long time no see.
I've put the guards outside to sleep for a while.

FUYUTSUKI:
This will cost you your life.

Kaji:
I just want to get closer to the truth within myself.
Besides, it looks like they'll find out
that I diverted the sample of Adam to Commander Ikari,
so I have to guard my own interests too,
or various bad things will happen.

ep 23/23' wrote:??:
That man is smart enough to know the significance
of why we allowed Fuyutsuki to return safely.

??:
We need another human sacrifice to counter Ikari.

KEEL:
And we need someone who knows the truth.

What SS said. It was just a random assassin working for SEELE that took care of him.

Though, in the manga, it was Gendo, but that's a whole other box of thin mints, there.

Asked. Answered. Done.

It was Maya. Being an underling of SEELE, they would most likely be a higher-up in NERV to find the dirt on top secret stuff. Maya was one of the top three "bridge bunnies" in the show, and was seen assisting Ritsuko in stopping the angel, so one could presume that she was considered important by NERV's top scientist. Also, she knew Kaji on enough of a level to suffer his flirtations, so I imagine getting him alone with her to kill him might have been possible. And for the argument of her being to afraid to fight back against the soldiers in EoE, fighting a large group of people firing at you first is different then taking one possibly unarmed man completely off guard and shooting him.

Of course, it could also have been one of the two Section agents who escorted Misato to the prison cell, since only one of them returned with her gun. But I like my theory better.