The problem faced with in this part of the game is which element should be more prominent: the succesfull ending of the story or the gameplay pacing. Game designers will invariably prefer gameplay pacing, because a boss fight can provide a challenge more than once, whereas a story ending can only work succesfully once, meaning any replay attempt of the game will be more boring, with the player knowing the outcome already.
Furthermore, it is essential for the succesful completion of the story and the resulting evaluation that there is a peek in gameplay constancy at the end of certain sections. The Energy temple (from your example) would be dull without a boss fight, the dragging back and forth of the orbs would become tedious and the final part would be anticlimactic, destroying the careful construction of the whole energy temple and invalidating its constancy of proper music, atmosphere and anticipation. The story alone would not be enough of a reward for the completion here, because the way the temple is constructed demands a "crescendo" event. Touching a crystal would only resolve the story aspect, not the required gameplay crescendo.
And adding to that last point is the notice that the storyline of games constantly creates an opposition. There is a goal, usually personified in an enemy (boss), which is superior to the other enemies that you face. The defeat of Mephistophiles at the end of Neverwinter Nights is an example of a boss fight, not a resolution without one. The player is pitted against a mighty devil of the most powerful kind (thus a boss). Just because the option of guile (learning his true name for a load of money) enables you to instantly kill him, does not mean that you do not defeat him.
This is the important difference between the two options you voice. Game designers have ocasionally tried to forego boss fights and create anti-climax resolutions, but they have thus far not been able to fully replace the invention of the "boss" with something else.
