Was I supposed to perform the Blackroot ritual three times?

You don't miss any powers by performing it only twice instead of three times. (In fact, it's possible to perform the ritual only one time, granting both powers at once.)

After one Source point, performing the ritual grants you Spirit Vision.

After two Source points, as you suspected, performing the ritual grants you Source Vampirism.

After three Source points, performing the ritual will simply grant some dialogue with your god. Upon your return, you'll find Meistr Siva dead.

This video shows the intended progression: