Don't dead dwarves typically end up with upper bodies missing in their descriptions? Sounds to me like that is some kind of thing Toady had to do to make death work with the new body system. I imagine after you revive them they always go "Yay! I'm alive! Oh wait I'm missing one of the vital body sections, looks like I'm dead"
While DC was able to revive dead dwarves in the past, from what I hear the new body system is still a bit of a mystery to memory editors, and runesmith currently can't restore missing body parts. So once it's dead, and the game removes it's upper body for whatever reason it does, it's staying dead.
As for the siege thing you may be out of luck. Sounds to me like something did something that would normally cause the game to turn off the siege flag, but didn't happen correctly. It could have been something as simple as something dying improperly and not counting down some counter the game uses to keep track of when to turn the flag off, to something as convoluted and freak as a bit getting corrupted in memory. I haven't heard of endless sieges myself though, at least not without a goblin or troll or something idling around someplace. Did you delete any gobbos or anything while the siege was still active? If so runesmith forcing the critter dead may have broken the siege flag somehow.
I hear sieges that last a really long time sometimes just get bored and leave. You could always wait and pray that that happens in such a way that it resets the flag properly on it's own. Or since siegers don't seem to be hindered by other siegers, (or at least other siegers from another civ) see if another goblin siege shows up. If you manage to beat it the flag might get properly reset when that one flees.