Why didn’t the Didact just use the Composer to strictly vaporize the Flood? 
I understand it’s purpose was to digitize organic life but couldn’t he have also used it as a weapon strictly to vaporize the organic life of the flood? It worked wonders against New Phoenix along with an entire human space station. What was stopping him?
I don’t think the Composer worked on the Flood since they aren’t organic life. At least, not anymore. That’s why the Halos didn’t kill them. It just killed their food (organic life).
The Composer works in a similar manner, I think.
The Halos kill Flood too… that’s been shown numerous times since Cortana’s generalized comment in CE.
Just not infection forms, I believe, which is why the “food” needs to be killed too.
The Composer was never intended to be a weapon. It is used to preserve the minds of the dead and create AIs, originally a potential way to grant the Forerunners immortality.
Only when the Didact, in his insane mindset, decided to use it as a weapon to compose Humanity was its dark side function revealed.
Also, the Ur-Didact was only active for a small part of the war. His goal was immunity at first, not an army. The IsoDidact wouldn’t have such an interest in the Composer. For him, it is just a failed device that the Master Builder used a couple times to preserve those being infected.
Silentium made it clear that it was the Star Roads that were of the most effect against the forerunners. While the composer may have been usable as a weapon against the flood, it would not have won them the war.
I also don’t believe all composers are as…flesh incinerating as the one the didact used. The smaller ones used before didn’t seem to include this. It might be a result of upscaling, or the didact actually weaponised it.
That was actually the original plan of the Composer. It’d be used to digitize what was left of the Forerunner minds in the Flood biomass of all kinds, saving them from the Flood. New organic bodies would be then given to them. The problem came though with the organic bodies as the Librarian tells us.
Urbane, the Composer was described as a crude tool. It’s been described as painful no matter how gentle you are with it. If you take the process slower with intermediary devices, it’s less painful and more accurate. However, if you want to be quick about with no regard for whoever is being subjected to the Composer’s energies, it will be extremely messy and painful as we have seen with the Ur-Didact and Mendicant Bias.