Eh. I see what you're trying to get at, but I'd like to point out Gunbuster as my counterpoint. Those people were willing to win at the cost of planets. They took Jupiter, turned it into a bomb, and blew up the galaxy to save the human race. You can't half ass this stuff, and that's exactly what's wrong with this episode of Yamato. Every decision made in this episode was outstandingly stupid.
I realize I'm doing that thing I do where I dare point out stupid things about shows you all love, but this entire episode was a tactical blunder of massive proportions.
First, I'm gonna point out what Jex said about what this series is. It's not interested in realpolitik analysis. When this series was originally made in the 70s, the Yamato was a redemptive symbol for Japan, a tool of aggressive war recreated into a savior of humanity that stands for its best qualities. If they used the Wave Motion Gun indiscriminately, it'd reflect that Japan had learned nothing from the experience of war. The Yamato exists not to conquer, but to save mankind from extinction. So even if it were the most efficient method, it's not ideologically viable for the creators to endorse it.
Secondly, concerning turning Gamillas into scorched earth, the Yamato's situation is wholly dissimilar from the situation mankind faces in Gunbuster. The aliens in that show are an animalistic force that can't be reasoned with, and humanity still has its infrastructure. They have no choice but to commit to total war, because the alternative is annihilation. If they succeed, all of mankind will be saved.
Gamillas is an aggressive empire, but it's not impossible to reach peace. More importantly, if the Yamato does not complete its lengthy journey as quickly as possible, they will be the only members of humanity left. They barely have time for this Pluto mission, which is only really being attempted for the sake of keeping Earth's morale from collapsing completely. If they attempt to bring down an empire spanning numerous star systems with a single vessel and somehow succeed, they will reduce mankind's population to under 1,000 people: the equivalent of choosing to engage in total nuclear war. While if they can successfully reach Iskandar, they can save millions of lives and keep the Wave Motion Gun as a deterrent to future invasions, the way that some third-world nations today attempt nuclear weapons programs.