If the brothers did not legitimately think that Joseph deserved the death penalty and wanted to kill him anyway, you wouldn’t expect them to care about this either. If they did legitimately think thatJoseph deserved the death penalty then we can perhaps apply the following passage from Berachot 10a:
What did the Holy One, blessed be He, do? He brought sufferings upon Hezekiah and then said to Isaiah, Go visit the sick. For so it says, In those days was Hezekiah sick unto death. And Isaiah the prophet, son of Amoz, came to him and said unto him, Thus saith the Lord, Set thy house in order, for thou shalt die and not live etc. What is the meaning of ‘thou shalt die and not live’? Thou shalt die in this world and not live in the world to come. He said to him: Why so bad? He replied: Because you did not try to have children. He said: The reason was because I saw by the holy spirit that the children issuing from me would not be virtuous. He said to him: What have you to do with the secrets of the All-Merciful? You should have done what you were commanded, and let the Holy One, blessed be He, do that which pleases Him.
(Soncino translation, my emphasis)
Under this approach it doesn’t matter whether There are supposed to be 12 tribes or not. Man’s job is to fulfill his duties; it is God’s job to make sure everything happens in accordance with the master plan.