This has always bothered meThis post contains spoilers for the plot of Halo, if that bothers you.
In Halo, our super-soldier lead stumbles across an ancient device called "Halo". It is a giant artificial ring, with the power to destroy a galaxy. It was built to contain the flood, a species of creature which infect and take over other sentient life, and stop them from spreading. If they were to break free, the option was there to destroy the entire galaxy.
So why not just blow up all the halos? As far as we know, the only place the flood exist is on the halos, and considering the forerunners are willing to obliterate a galaxy to destroy them, they don't seem to worry about extinction. What makes the galaxy destruction worse is that the flood are sentient when in large enough numbers. Galaxy destruction is a TERRIBLE solution. It won't save your species because, you know, you've BLOWN UP THE GALAXY and it will wipe out the sentient force that would have replaced it....
Maybe there are answers to all these things- they were not apparent in the games.