I'm aware the following is a suggestion, but it's probably just a single line of code and a minute of work, so I'll just go for it:
Toady, you said that when a dwarf in the fortress mode turns into a werewolf and kills a fellow dwarf, he'll be marked as an enemy of the civilisation and killed - even if he changes back to dwarf form in the meantime. Now... how about instead of making him an enemy, making him a criminal and imprison him for murder? Leave it for the player to decide whether they want to execute the murderer (via the kill command... presuming it gets fixed).
I just can't get behind the idea of dwarves killing their friend dwarf just because he's cursed. When the dwarf changes back to his dwarf form, he's friendly and harmless - they can't just butcher him! Lycanthropy should be handled as a criminal act, not an act of war. The code for murder and imprisonment is already in the game but is only rarely used - why not use it here? The game gains a bit more variety and everyone wins!
I know it's not an ideal solution (ideally a werewolf in a wolf form would be an enemy, in dwarf form a criminal) but as a placeholder it just seems better that the other extreme (kill him!).