I'm going to boil this down very simply to try and bring an end to this.
If you wish to automatically split the second disk into a new array with
a new uuid, you must update the metadata on that disk to indicate you
have done so, and if you end up connecting that second disk in the
future without the first, it must still show up with the new uuid.
Which uuid it appears as must not depend on which one was plugged in
first.

That however, would be a new feature of the plug and play system outside
the scope of mdadm.  If you want to automatically split the disk off
into a new array after the desync has been detected, that would be nice,
but fixing the bug in mdadm is as simple as having it detect the
conflicting metadata on the second disk caused by the divergence, and
fixing said metadata to agree with the metadata in the array, which says
that disk is failed.

At that point whether some other component automatically invokes mdadm
to move the second disk to a brand new array, or the admin has to by
hand, I don't really care.

-- 
array with conflicting changes is assembled with data corruption/silent loss
https://bugs.launchpad.net/bugs/557429
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