Yes Morganthe's prophecy did come true, in my opinion.
The Mirror will Break (she destroyed mirror lake)
The Horn will call (Huracan the horned one called to Xibalba)
From the shadows I strike (I never got that one I think that is when she got really mad and mastered Shadow)
And the Sky will fall (Xibalba destroyed Azteca)
Alexander Stormglade lvl 100
Alternate reading of the prophecy for the last 2 parts: From the shadows I strike (refers to your wizard learning Shadow magic to defeat her) And the Sky will fall (Morganthe's destruction, falling, sending her spinning off into space)
She always thought the prophecy was about her, and she was chosen. Others doubted the prophecy was about her and it seems like it was actually referring to our wizard. Cobb seems to confirm that some.