I agree it's confusing but I came across this interesting explanation:

When you fill out a form in English, quite often you are asked about your: MARITAL STATUS. Take note of the word: STATUS. This word refers to your "state". 

The same applies in Spanish. You are asked for your: ESTADO CIVIL. So, as you can see, the Spanish word for STATUS is ESTADO, which comes directly from the verb ESTAR. So, in the eyes of the law, marriage is a state of being, just as is being single, separated, divorced or whatever. It is for that reason that in Spain when people refer to the marital status they use the verb ESTAR. It has nothing to do with permanent or temporary things.

It also helps to see the contrast side by side:

SER:  Who is someone:  Ella es su esposa.  (She is his wife).

ESTAR: Relationship status, as on Facebook: Ellla está casado. (She is married).

 It helps to make a list of the different relationhip statuses used in the examples in the above lesson.