Leandro-Z, I think you are on the wrong track – maybe there is a similar expression in Spanish that has a different meaning.
[FONT=MS Pゴシック]Yes, it is an idiomatic expression. It is similar to “Don’t take this the wrong way.” It means that if someone says something to you because they are being helpful or generous, you should try not to be offended or take it badly, even if you think they should not be saying that kind of thing to you. The “spirit” in this case are the good intentions the person has when they say something.[/FONT]
[FONT=MS Pゴシック]In this example, the girl probably says, “Take it in the spirit it is intended.” meaning, she is trying to help the boy. You can understand why the boy might get angry if someone told him that his girlfriend was hiding something. The girl knows this, so she asks the boy to remember that she is just trying to help him, so he should not be angry.[/FONT]
The first example that came to my mind was something like, "Please take this advice in spirit it was intended. I am trying to help you, not talk down to you or boss you around."