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Any idea why the game shuts down in that kind of situations?

There may be a problem with the inventory files in your save game, or it could be something to do with how the game keeps track of your removed stuff. If you drop everything yourself first, does this crash still occur?

For the guards in the dwarven hall, you can kill them using an area effect spell that does not need a target (Poison Cloud) to avoid the reputation drop (cast it near but not on them).