The following is the original line from BANNER:

> Are you here to kill me, Ms.Romanoff?  
>’Cause that’s not going to work out for everyone.

I'm only going to focus on the second line.  This is a comedic line.  Banner is not absolutely invincible, but from experience, he knows he's not likely to get hurt.  Here's the original and the paraphrase, with phrases marked in brackets to correlate the two:

 - 1[’Cause] 2[that’s not] going to 3[work out] 4[for everyone].
 - 1[Because] 2[trying to kill me is not] going to 3[end nicely] 4[because either you'll succeed and that won't be so good for me, or I'll turn into the Hulk and create all kind of havoc, damage, and possibly harm, which won't be good for you, and I don't really think you'll be able to kill me - more than likely, the 2nd scenario will occur].

Here are some language notes:

 - The word combination "work out" is a "phrasal verb" that in this case means [to be successful](http://www.macmillandictionary.com/us/dictionary/american/work-out#work-out_10) or [end nicely](http://www.usingenglish.com/reference/phrasal-verbs/work+out.html).
 - It's somewhat idiomatic to say something like,  "I hope this works out (for me; for both of us; for all of us)" or "Don't worry, it's all going to work out (for you; for both of us; for all of us)".
 - As @DamkerngT noted, "That's not going to end nicely **for everyone**" has a double meaning. Let's take a more simple sentence "It's not going to be fun for everyone" means "at least one person will not have fun" but it also implies the possibility that "nobody will have fun".  So there is also the sense that even though Banner doesn't believe he'll be killed, if she tried to kill him, it would also not work out for him either since he doesn't want to turn into the hulk.

Compare to a hypothetical scene from a Batman comic where Batman is surrounded by four thugs carrying sticks, chains and knives, and Batman says, "I think you boys should put away your toys and go home before someone gets hurt."