My thoughts:
First, the
BG2 joinable NPCs:
Imoen - needs to be kept alive (somehow), unless someone does a major mod where here role can be taken by another
BG1 mage
. One trick would be that if she dies, the dead one turns into a dead doppelganger - you don't find out what actually happened to her until the begining of
BG2 
(this idea could be used for someone else, but shouldn't be used more than once, if at all).
Jaheira & Minsc - if they permanently die prior to
BG2 OR are not in the party - then they stay dead/are not present in the dungeon.
Viconia - if she dies permanently, then her place on the stake is either empty (delete the whole scene - or she is replaced by someone else) - actually, considering how soon you can get her after leaving Irenicus' dungeon, I suggest that if she is in the party at the end of
BG1, she should end up in one of cages in the dungeon, and the gov dist. scene be either removed, or have her kidnapped in Athkatla and dragged off to be burnt.
Edwin - a lot more complicated, as he's needed for the thief stronghold quests - one solution is that towards the end of
BG1 he takes his leave ("I have business in the south etc.") The more complicated option is that he stays with the party and ends up in a cage, and his role in the thieve's guild is replaced by someone else.
The
BG1 NPCs that show up (or are mentioned) in
BG2 but are not joinable (except by mod).
Khalid & Dynaheir - If they die prior to
BG2 then references to them in the dungeon (Minsc's statement, Khalid's body) should be removed Minsc's and Jaheira's dialogue would need to reflect this as well.
Xzar and Montaron - should leave the party prior to the beginning of
BG1 under orders from their superiors - if they have been travelling with CHARNAME for a while then CHARNAME should have a reasonable idea who these 'superiors' are and should be cool with it, and should understand why ignoring such a 'request' is a bad idea
.
Quayle - again, should leave on some pre-text (he's just inherited a circus). If he died, either the whole circus quest vanishes, or just he & Aerie vanish (possibly replace Aerie with a non-joinable commoner?).
Faldorn - gets summomed away to the Trademeet druid grove - if dead gets replaced - perhaps by one of the other Shadow druids from
BG1, if they're still alive!
Tiax - um.. either he wanders off prior to
BG2, or, he is present in a cage "How is mighty Tiax going to rule from this cage - he commands that you release him", and gets grabbed by the cowled wizards at the same time that Imoen is
Garrick - well, he doesn't do a lot in
BG2, if he was in
BG1 he should be found dead in the dungeon (or as a twisted thing in a bell jar), if he died in
BG1 he stays dead, in either case, his appearance in
BG2 could be removed.
Coran & Safana - Safana's dialogue implies some sort of grudge with CHARNAME - so maybe she has a row and leaves prior to
BG2, and love-smitten Coran follows her.
Ajantis - as his only role in
BG2 is to have his corpse IDed, and not even by CHARNAME, then I think, like Garrick, if he dies, he stays dead, otherwise his body is found in the dungeon, and the dead paladin that Keldorn or Anomen ID is given a different name.
BG1 NPCs that don't show in
BG2 (the tutorial doesn't count).
By default, if any of these die, they stay dead, otherwise their corpse, or twisted, barely alive body is found in Irenicus' dungeon.
However, in at least two cases (Alora & Kivan) there are mods that provide them as joinable NPCs in
BG2, in which case they should stay with the party (and be found in a cage in the dungeon) - the mods may need a bit of modding for this.
Ok, with hindsight, maybe just magically keeping required NPCs alive is a lot easier
Charles
Impossible....
