Re: Who would you let Joss Whedon kill in Avengers 2?
If anyone major had to die in the second film I would say Nick Fury.
It effectively cuts off the head of the 'avengers initiative', leaving someone to fill his very large shoes. It also immediately raises the emotional stakes for the third film where the heroes have to work against the speed bump of working with/under someone who they don't know/trust/have that relationship with.
Also if you were to throw in a macguffin shaped 'piece of information' that only Fury was privy to (ie. the whereabouts of a of something that would save the day etc.) it gives our heroes a physical obstacle to work against/for.
If you're going to kill of any of the primary four Avengers (Cap, IM, Hulk, or Thor) then it shouldn't happen until the Avengers 3. That way the studio has used up the contract of the chosen actor (each actor will have been in at least 6 films by that time), and the death of the character can come in the form of a final sacrifice that saves the world from whichever 'Ultimate evil' they happen to be fighting.
That's how I would do it, anyway.