: Protocol. When the Flood were contained he could do whatevs, once they were
: free he had to stick to his programmed "containment protocol"
: plus, we don't know if vacuum kills Flood spores....Forerunner didn't want
: to risk having chunks of Halos floating around with viable Flood spores on
: them

I'm inclined to think that the vacuum is lethal to Flood, in that we've never seen them operate in a vacuum and they have to have some method of respiration. But my guess is given what we learned in the Forerunner Trilogy, combined with little details throughout the original games, that the spores themselves might be a different matter--able to remain inert or dormant in the absence of stimuli or a place to reproduce.

343GS mentions evacuating all matter from contained sections in the CEA terminals, but it's not specified in what capacity this action is done--perhaps it's not to kill Flood, but to quarantine them to a certain section by depriving it of areas to expand to.

As to why 343GS didn't do these things in CE (aside from the fact that none of these capabilities had been established)... there's several options. One is that he actually did attempt it. After all we only visited a tiny portion of the ring, and it seems likely the Flood could have spread pretty rapidly. I'd say that the control room diagram of the ring suggests as much (I can't think of what else those red zones indicate.) But perhaps things spiraled out of control so quickly, and the presence of not one but two vessels that could allow them to escape the ring forced him to escalate protocol.

The other possibility is he wasn't thinking straight. Or it could be both in equal measure. We know Spark wasn't all there long before CE rolled around.