For me, it was really annoying.
At first I think it was a huge mistake, absurd and misplaced.

After think about it for a while, I must say I see a purpose in it.
I think its purpose is make you to share Neil's frustration.
I believe the idea is get you in the skin of Neil and make you think:
- I'm lost fighting with zombies and getting pull back by traps while Eva is hurting John by erasing River.

In addition, by creating bad feelings about Eva, the game developers also create suspense on the ending of game.

I still hate this action scene, I wish it wasn't there, but I can't say is misplaced or it is a stupid mistake any more.

What do you think about this ?

It's been a while since I played, but I remember that scene and felt it was well placed. I can't exactly remember the context, but [spoiler]wasn't it a diversion by your other little dream scientist person? It seemed like it evoked a bit of frantic pace to an otherwise slower paced experience. [/spoiler]

Well, yes. It was other little dream scientist person doing.
The other dream scientist name was Eva.

At that point of the game I was no looking for action, I was craving for the ending of the story.

I do agree that it went on a tad too long at NASA. I was on autopilot at that point just wanting to see the ending as I felt like the story had been told.

It was horribly misplaced. I have no idea why an action sequence (a badly done one at that) would appear at a point in the game where you're just expecting the ending.

After having to endure that I no longer cared about the rest of the story. It ruins the whole game.