(1) Yes, it is an instakill spell, but that doesn't preclude it having a reasonable save. You have to wonder, if even on save it does 15,000 damage, does it seem likely that this was the intended behavior? Keep in mind that it's not as if all Arcanum damage spells have saves, harm doesn't for example. If they wanted disintegrate to always kill, why bother having a save at all? Given this lack of logic and the inconsistency with the manual (which says you can survive disintegrate, correct me if I'm wrong), I would say it is very likely that Disintegrate has a bug. To me it seems more of a question what is the correct fix than anything. But if this is not a very convincing argument I won't push any further since I'm not the one who has to hex edit the game.
Yes, I just checked, a critter with 20 of constitution was instantly killed, no difference. But what do you propose? It's actually strange, you see, a critter can save against Dominate Will for example, if it has high willpower (the spell won't work at all), but it doesn't save against Disintergrate with high constitution. The damage is just too high to save, I guess.
(2) My preferred solution to this would be to force the familiar to the top, outside ledge of the pit for the duration of the fight (eg let it be a neutral observer that hangs outside the pit) and then let it rejoin the party automatically when the player is completely done (note btw that the familiar does not count towards the party limit so you shouldn't have much error checking to do). If this is not possible, then don't worry about it. I agree that the familiar counts as a separate entity from the caster and that you should have to enter the pit without it.
The pit is a different map, and when player teleports to different map all his followers do the same. I can add a dialog to familiar, so it can wait outside, but again, does it make sense? I'm not sure, what other people think about this issue?