The Domain wasn't destroyed.
Being a living Precursor, it's allied with the Flood; therefore, it simply prevented the Ur-Didact from accessing it, in order to simply screw with him (that, or it kept telling him terrible knock-knock jokes over the past 100,000 years). The Gravemind's taunt to the Librarian was all a lie. Guilty Spark tried to access it, but was rejected, as shown in the terminals of Anniversary. Once John and Cortana came along, however, the Domain, following its own agenda, allowed John to access it.- It's clear that *some* of what's said about the Domain is lies, from the fact that the Ur-Didact claims to have had contact with his and the Librarian's descendants.
Not all the Precursors were evil.
The ones that created were initially benevolent, but some psychos managed to get through and started being xenocidal with them instead. The Forerunners had enough of that and retaliated, but ending up equating the good ones with the bad ones and wiping most of them out. Those that went survived and went into stasis were then further corrupted by their resurrection as the Flood. In short, coming back wrong made them even more omnicidal than the original bad ones originally were, leading to their second war with the Forerunners.- Halo: Point of Light reveals that their were benevolent Precursors and that not all of them either were in on the Flood plan or were aware of it and implies the Primordial and other like-minded Precursors do not represent the will of the Precursors as a whole (it delighted in death and destruction) and that it may be in the minority among the Precursors' views regarding the Forerunners and their creations. It also implies that the Flood was the result of those Precursors' reincarnation process being corrupted by their negative emotional and mental state and desire for revenge against their creations.
The Precursor "anchors" lead to the Warp or the Shroud or some other Lovecraftian-esque realm.
The Precursors left behind mysterious deep-space artifacts known as "anchors" — large, anomalous masses which released no radiation. They were generally regarded as unstable and dangerous; the Forerunners had recorded strange phenomena near the masses, including ships vanishing and surviving crews suffering severe mental trauma, requiring extensive proto-geometric therapy to restore their minds' neural topology to its normal state. Sounds like something straight out H.P Lovecraft, Warhammer or Stellaris.