He is crazy about her. He is head over heels in love with her. He loves her. She's not quite sure which expression he would use to qualify it but it's definitely here.
And she knows it.

It's in the way he sometimes looks at her with pure lust when he thinks she's too busy bantering or arguing with Tony, playing tricks with Abby to the poor oblivious McGee.
But she sees the looks, she feels his eyes on her. Sometimes when he's close to her she even feels the want irradiating from him, his body, the want to send the two other agents far away from the bullpen and bend her over her desk to claim her as his.

She feels it, she knows it.

But it's also in a more gentle, more tender way.
When he sees her exhausted or touched by a hard case, she sees the concern in his eyes, she also feels the want from him to pull her in his arms whispering words of comfort and kissing her temple just like he can do so easily for Abby without a second thought.

She sees all of this and she feels all of this.
And she wants nothing more than to let him do all these things and more... yeah... much more. She knows with just a step from her to him he would be hers and she would be his. He needs her too much and he would forget about his damn rule in a heartbeat.

And she really wants to take that step but she waits.
She waits because she wants him for so long, so much longer than he do that it's impossible he can already feel half the agony she's gone through by loving him when he saw her just as an agent, a good agent, one he would be proud of later but still, just an agent not even a woman.

Since she saw the change, she waits. And the day she'll look him in the eye and see that the excitement of being in love again has changed into the pain of not having the one you love by your side, she will move and she will show him and it will be great for both of them.
But not before that. NOT BEFORE THAT !!!

Cruel ? maybe ... Masochist ? for sure !!!
But Gibbs needs to understand that he can't live without Kate 'cause Kate ... well SHE already knows it.