They HAD to let the Forerunners win cause of the huge technology gap. The Precursors created or advanced the Forerunners so much that they consider it “Giving them life.” Why would the Forerunners rebel? We don’t know, but the Forerunners were civilized and noble people they would not automatically rebel just because they felt like it. Even if the Forerunners tried to rebel the Precursors could gun them down instantly without hesitation cause it endangers their lives.
Lets compare it to a genetically enhanced monkey. If we make the monkey capable of knowing right and wrong, but it tried to break out of its containment cell anyway. It only has its fists and it does it even know what a gun is, we could gun it down as soon as it endangers someone or sedate it which is what the Precursors could have done and WOULD have done that if it was needed.
The Precursors had technology which made their buildings invincible in our terms. Nothing and I mean NOTHING in ours and the Forerunners’ arsenal could hurt a single object of theirs excluding the Halo Array. A single Precursor ship can take on the entire UNSC, and Covenant fleet on and win without a scratch. I do not even think the Forerunners can take on a single ship due to the invincible material (although mass focus fire may do something). Look how long it took the Forerunners to develop the technology for the Halo Array cause this the only way to damage Precursor objects and structures. When the Precursor-Forerunner war broke out they were probably only a few hundred planets MAYBE above one thousand. The Forerunners are probably laughable beings compared to a single Precursor which ONE of them is a threat to the entire race (read cryptum). The Precursors made the Flood…the thing that can assimilate entire species and have infinite intelligence. The humans had to turn to the Timeless One, the only Precursor left, for help and they won and drove off the Flood while fighting the Forerunners.
TL;DR The Precursors HAD to have let the Forerunners win the war due to technology issues and life endangerment.