"Que pense com sua cabeça."
Surely this is just a fragment of longer sentence, though, because "pense" is 3rd person present subjunctive and therefore should only appear in a subordinate clause, or so Paulenrique keeps telling me when I make mistakes with the subjunctive. :-). Of course other "correct" translations don't really work, like "that he thinks with your head" and "that you think with his head", etc., but from a purely linguistic point of view they are fine. :-)
That's right. The subject is omited.
But it's twice tricky, an entire main clause was omited. So imperative and subjunctive aren't clear here, and they will depend on what was omited.
It could be:
1 - "Ele que pense com sua cabeça". In this case, with "ele" as subject, It's an upset imperative answer, maybe for someone who asked a question. Like: "Eu não vou responder isso, ele que pense com sua cabeça" = I won't answer that, he think that with his own head (I'm sorry, I'm not a native english speaker, so I can't be sure I wrote it ok, but it's an imperative order given to a third person).
This could be inverted like this: "Que ele pense com sua cabeça". That's still imperative, but not so upset as the previous. It could have a main clause omited: "Eu quero que ele pense....".
2 - "Quero alguém que pense com sua cabeça". In this case, the main clause was omited. It makes the subordinate clause subjunctive: I want someone who thinks with their own head.
In this case, subjunctive is not an obligation, indicative could be used as well: "Que pensa com sua cabeça.". The difference here between this indicative and the subjunctive is subtle. The indicative is more likely to presume that person indeed exist, like many other persons I've known before. The subjunctive would express a more hypothetical person, meaning it's hard to find someone like that, almost a myth.
So, to summarize, the difference here is between:
1 - Want that somebody think. Imperative. "Quero que alguém pense"
2 - Want somebody who thinks. Subjunctive. "Quero alguém que pense".