It could certainly be said that Misato was correct. Kaoru did have less of a desire for life, as evidenced by his lack luster approuch to merging with Lillith, who he thought was Adam at the time. He seemed deeply sympathetic towards those wacky lillim and was verbally expressing self doubt. "Must those born of Adam return to Adam" blah blah blah. However, it seems to be only one of several factors that led him to his final decision.
It seemed to me that Misato was once again projecting, as she often did throughout the series. One final time, she voiced an opinion that reflected her personal feelings -- in this case, hatred for the angels -- without regard for the feelings of those around her. At that final moment, she seemed to represent everyone who would never understand the level of friendship Kaoru and Shinji had, because they hadn't witnessed it first hand.
That said, there can be only one way to end the manga...
Shinji comes back, finds Asuka, and the two make their way down a lonely beach together... and come upon Kaoru's head.
...not that head, fangirls! o__O