The problem with any potential Forerunner-Human War is the length of said war. The longer the war drags out between the Human-San Shyuum Alliance and the Forerunner Ecumene, the more power and wealth the Builders obtain. And the more power and wealth the Builders get, the more the Ecumene will want to wipe out humanity in its entirety for the Forerunner lives lost compared to how they were only spared because of the Flood "Cure" they believed exists. An Ecumene solely focused on smashing the Alliance is going to achieve its goal, it is only a question of time and just how much they are willing to throw at the Alliance seeing as how it was noted by the Didact.
During the war, the Builders built more weapons and ships then were necessary. Besides supplying the Warrior-Servants with arguably an endless supply chain. The Alliance would inevitably lose as its unlikely they could take Maethrillian. They'd have to first pass through the countless fleets just to get to the Ecumene's capital and quite possibly the Maginot Line. And in the event they get passed the weapons that basically snipe them in slipspace travel. Upon arriving at Maethrillian, they'd have to contend with the Capital Defense Fleet and the supporting fleets that would likely be minutes if not mere seconds away and the Alliance forces would be trapped.
I am a fan of Ancient Humanity and the San Shyuum just as much as the next hardcore expanded universe fan. However there is no conceivable way that they would win. The Ecumene puts out more then the Alliance probably can and we aren't even considering the Forerunners mastery over slipspace and astroengineering. The Halo Array is unlikely to be built in this scenario without the Flood, but seeing as how the Didact is a strong believer in Forerunner security. His plans for the Shield Worlds would be supported and with each fortress world made. That makes it one more planet the Alliance would have to worry about in Ecumene and formerly controlled Alliance space.