Regarding Kotomine and Assassin's death.
Well, I can perfectly see a plot where Assassin's death serves a role for Tosaka and Kotomine.

Assassin dead, other masters would think he's out of the game, when he in fact will target masters. He's highly train in many arts as Kiritsugu stated, so even without a servant, he can clearly have the upper hand in any situation when a master isn't protected by his servant.

This idea isn't really in line with what we know of archer in the game and FSN anime, mainly because we do not know what will happen with Tosaka. Or it might only work with Tosaka...