I think this can safely be considered a miscommunication between the devs and Tom.
There are two separate issues here.
One is the issue of the realm merger. In my opinion, nothing about it was friendly or peaceful, so this point is mitigated somewhat.
Second is the fact that the player accused exploited what he knew was a loophole to flip his duchy. His earlier post gives me the feeling he knew he shouldn't have been able to flip the last duchy in the realm, when he said he felt the capital flip was a bug. Surely then he would have known you cannot change allegiance with the only duchy remaining.
