In the Fourth Horseman Pt 2 the Prior that got disabled began preaching to Orlin when Orlin begun to speak. Naturally we all listened to Orlin and tuned out to what the Prior was saying... but he did say some very important stuff.
Now, I'm at work so I can't really look up his exact words... But he said that the O'ri were born from the rift (no doubt the moment the Alterrans split off) and that the Alterrans travelled the universe and spread death and destruction wherever they went, hence evil. What if the O'ri are destroying the Ancients in as a precautionary measure to protect themselves? Let's look at what the Ancients brought the Universe.
1. The Wraith - Space vamps with a bad attitude. Death and destruction.
2. The "groundhog day" device - A device that loops time. Pure chaos here, ignoring of course the theory that it was made to come up with a cure for the plague
3. The Dakara weapon - WMD of the great scale we've seen so far
4. The Holy Grail - Anti-ascendant WMD, ignoring of course that it was made by a rogue Ancient
5. The Asurans - a freaky spin off of a virus
6. The gate network - Ultimately allowing the Goa'uld to take control of the entire galaxy. I doubt their homeworld would've given them this capacity alone.
7. The gate warping device Anubis used
Now, my theory is that the Ancients like fighting... and so they go around picking fights and creating enemies. It's possible even that the Wraith and O'ri were the only enemies capable of overpowering them. *shrugs*
Either that or the Ancients just had so many misguided scientific ventures that went wrong. After all, one would have quite a few mistakes after a few million years of advancement. The O'ri seem like the kind of race that would've ascended through meditation and spiritual means.