I know it was off the books, but it was still two DEA agents attempting to take down a drug kingpin. On the books, off the books, whatever, we know both Hank and Gomez loved the job and took their duty seriously enough that all that would matter to them is that they're the lawmen bringing justice to a criminal who richly deserves it. I mean, yeah, it's a shame that he got killed, but we kind of all saw that coming, didn't we? And, for what it's worth, I don't think he or Hank would've balked at dying in the line of duty.
Walt is using the M60 to take out the nazis and Jesse. Walt will hear "Heisenberg" is back cooking, thanks to Jesse cooking for the nazis, and his pride will cause him to come back and stop them.
That's my current theory too. Walt clearly hates Jesse now, since he blames him for Hank's death and, later, the destruction of his entire life. The blue meth's gonna show up with a purity comparable to his own cooks', and he's gonna know that Jesse's still alive and Todd & the gang haven't delivered on their end of the bargain to eventually kill him. So having basically nothing left but his seething rage at Jesse, he goes back to kill Jack, Todd, Jesse, and everyone else in his way.
That still leaves the question of the ricin, though. I'm kind of hoping that Walt kills the Nazis and at first seems like he's rescuing Jesse, only to slip him the ricin sometime. How crazy would that be, for Walt to hate Jesse so much now that he'd offer him one final ray of hope just to snatch it away and kill him?