Didn't the Forerunners turn around and kill the Precursors? Not just kill them, but they hunted them into extinction, the only possible survivors having fled the galaxy.
That may have had an impact on their plans too. Even the most dedicated pacifist may change their tune when they and their entire species is facing oblivion.
Still interested on how the Forerunners could have managed to turn the tables like that though.
I've always assumed it was less what the Forerunners did and more what the Precursors didn't do. They were so confident in their place in the galaxy that when the Forerunner hit, they crumbled out of shock.
There's also the question of their technology; I'm guessing that while neural physics was a pretty effective boon, if you're the biggest bad in the galaxy, you might not put much time into weaponry.