As a followup to this discussion thread I have posted an addin to the sandbox. If you have a problem with (or are just concerned about) Domino processes being killed from outside Domino, then use this addin. It will monitor all of the processes that are supposed to be running in a Domino partition (even if there is only one) and if a process that is supposed to be there suddenly isn’t then it will Panic the server.
This is an issue only for Domino on all Windows platforms. Domino for Unix platforms is able to handle this condition.