for all thoses asking why they didn't kill him while they have the weapon and started remove pieces....
let's imagine than a compagny create a device in san francisco, or tokyo (it was not supposed to be dangerous). this device went rogue, and need to be disposed.
but it's not possible to move it, and we are not sure what will happen if we destroyed it...
did you see the end crater/blast.. imagine this in a big city...
and why did i choose frisco or tokyo as city : because of the volcano...
in order to make all this works, you can assume they will choose geothermal energy, by sitting right above an old volcano (you can see the lava in the bottom of the crater)
now let's summarise.
first : we are not sur we will be able to destroy it (thousands of years have passed, rusting the iron part)
two : if we succeed to destroy it, it might explode, and we don't know the power of the blast, might erase the city
three : not only might erase the city, but can create a chain reaction with the volcano, might erase the country....
so let's incapcitate it instead, lock it in the basement of the tower, and create an order of religious guard to protect it 'forever'..
for the fact the cultists attack the player instead of the cube, it can easily be explain...
the order was created thousands years ago, by humains, with human intelligence, but at some point, they became what they are (probably in hope of immortality).
but by doing this, they loose humain thinking, and became animals, with on purpose : killing adventurers.
they don't know why they do this, they don't remember what they once guarded... they just know that they must kill adventurers.
there is a lot that we don't know, but i like it this way... we are intelligent people, we don't need to be taken by the hand and read the full story. if there is some blank, we can try to fill them, and may be at some point, an episode 2 will explain... nothing, and give more questions.
for the ending itself, i had some tough time, mostly being trapped between mobs, waiting the crushed... and can't remember how many times i was crushed...
but i still like it this way : it's different, difficult enough, some kind of 'last stand' of the game, trying to keep you a little longer...
(still a better ending than Mass Effect 3

)