Tom Cruise

The little girl that does appear at the end of the movie with Olga Kurylenko, is definitely not Suri Cruise (based on a few press photos taken of Suri being escorted onto the set of that movie), and is listed in the IMDB credits as "Julia's Child", played by a pair of child actresses, Abigail Lowe and Isabelle Lowe.

Of note, it was while Tom Cruise was away making this movie that Katie Holms filed for divorce.

ADDENDUM,

After re-watching the movie, I spotted a brief scene that I think could be Suri in the movie at the 01:35:47 mark.

In this scene, Tom Cruise and Morgan Freeman are discussing a plan to fly up into the Tet to blow it up, when a slight commotion behind them causes them to turn around as this small child squeezes through a group of the human survivors to get a better look at what they are doing. It's a rather inexplicable moment, interrupting what they are doing, and it's never explained who this child is or why this brief shot was in this movie.

So, on the left is a press photo taken of Suri as she was being escorted onto the NYC set of this movie, on June 12, 2012, and on the right is a video capture of the moment in the movie where that child squeezes through the crowd in that scene. Much shorter hair, but probably a wig, and the facial structure otherwise seems to be the same.

I will never understand how a father would choose to not be.. a father