Let it be = leave it alone (it's fine as it is, don't bother it, etc.)
So be it = (let it be done, this is the way it should be, "amen")
So be it = can also have a negative meaning (well, if that's the way it has to be, that's the way it has to be - we can't help it). "I don't like the arrangements you've made, but if that's the best you can do, so be it."