I've used Some Other Game Booster and there was a way to tell it what programs you wanted to keep running, so maybe look for an options area.
As for not being able to access the console: How are you joining the game after turning on the game booster?
Any shortcut needs to have those command line parameters. A desktop shortcut has the -console added in the properties, and if you join through Xfire, you have to add it in the game options (since launching the game through Xfire is just using a different shortcut).
If you start up Halo by clicking a link or icon in the game booster, it may be a different shortcut for halo.exe and needs the -console added somehow.
If it's none of that, try running the game booster as administrator if that's possible, which is something that's caused problems in the past for people when trying to play Halo and use Vent at the same time.