CJ spent much of the rest of series very lonely and so sad she almost pushed away the best thing that happen to her.

Too true. The end of the conversation is pretty blatant:

DONNA
I think Ben's great. I think you guys are great together. I hope it works.

C.J.
Have you seen us together?

DONNA
Not really. [pause] What should I be doing? Instead of this?

C.J.
Anything. You should... go to lectures and symposia and look for opportunities with non-profits and have one-night stands with reporters from the Post-Intelligencer and go on dates with what's-his-name from the Solicitor General's office, and anything that doesn't have to do with Josh Lyman.

DONNA
Wow. Okay. Let's not do this.

And all of those things CJ says sound very much like things CJ wants to do, and not necessarily what Donna wants from her life. (Indeed, she doesn't look particularly thrilled with the one night stand with Colin.)

But then, that is kind of a subtext of the episode. Everyone in that episode is projecting what they want onto other people, rather than being more realistic.