It is a true synonym NOW. I think the real sin is thinking you know everything about a word because you know the definition as it stands currently.
Mort- means death matters because that was the original meaning of the root for a word that was more closely tied to death/dying.
Now, we have broken ties with some roots and changed them to fit our needs. I'm glad that gives you the ability to look up a word then climb upon your horse and plant your righteous flag.
If you would like to get into etymology it is actually really interesting and I recommend it. But it isn't going to be as simple as mortified=embarrassed throughout the history of the word.