Why exactly is Yamato so pissed? Shit didn't go perfectly, but that's just part of war.
I can think of several reasons.
1) It's not just a case of things not going perfectly. They weren't exactly functioning on a tight deadline here; they easily could have contacted Youko instead of figuring out a new plan on their own, especially when the new plan was potentially high-casualty and they were explicitly ordered to minimize human deaths. While not necessarily a reason for anger in-and-of-itself, their blase attitude about it -- "Yeah we disobeyed orders, but we completed the objective so I don't see why you should care" -- is
not how you should respond to a reprimand from your CO.
2) Public Opinion of the fleet. PR may not
seem like it should be important, but on the scale of something like the Panama attack it can be. If attacks like this one -- killing humans in the five-digit range with minimal effort or warning -- becomes a
trend, well... Currently they're
only facing off against Britannia, which is all their orders say they should be doing. If they start racking up a six-digit kill-count and committing atrocities left and right, that's going to change. It might not result in the
entire world teaming up against them, but at the very least the other nations would likely agree to a ceasefire so that Britannia could free up their resources. Yes the Fleet would probably still win, but they gained a lot less here than what they'd lose in PR long-term if this became a trend. Best to nip it in the bud here than allow them to think that massive death tolls are acceptable as standard procedure.
3) It tips their hand. This is
far more firepower than they've previously displayed -- in fact it's only their second public, quantifiable display of strength. The original plan wouldn't have displayed much more of their capabilities than the attack on Pearl Harbor did.
4) While Yamato may be programmed not to value human life, she still feels that she
should (hence the order to minimize casualties in the first place).
Anyway, glad to see this back.