Disagree. The pagan philosophical traditions prized intellect and learning more than did early Christianity (which was very much an apocoliptic cult concerned with separating oneself from the world). A world where the Platonic Academies of Athens and other cities remain open-and great theological centers of the official state religion-will probably better preserve Classical literature and philosophy than OTL did.
As to what will take Christianity's place, I think it will most likely be some form of Neoplatonism, which incorporates Roman, Celtic, Greek, Egyptian, Semetic, and Germanic Gods as representatives of Neoplatonic divinities. The end result would probably look very similar to Hinduism.
I don't disagree with you on this. Early Christianity did much to shut down ancient centers of learning which helped to devastate the scholarly class. That being said, unless the POD leads to serious Roman reforms there will likely be a dark age. In my opinion said dark age would be worse.
In OTL neither the Roman republic nor the Roman empire were exactly beacons of stability. While Rome fell due to a combination of factors, the biggest reason for its eventual collapse was in my opinion its nearly perpetual state of civil war. Despite brief interludes of competence these gravely weakened the empire, as they gradually ground down its military, economic, and political power. These problems were amplified by plague which dramatically reduced the empire's population as well as its economic output. This was followed by de-urbanization, resulted in a loss of specialization of both crafts and general knowledge and a decline in trade. Inclimate weather further reduced the ability of the empire to produce economic surpluses, and support specialization. Worsening matters, it lead to mass migrations of "Barbarians" which stretched the ability of the empire to defend itself past the breaking point.
Now back to Christianity. The only praise I will give it, is that it was a centralizing agent in an era of decentralization and decay. The church (or for that instance churches or better yet islam) served as a unifying cultural force for wide geographic areas. Their influence brought them wealth, which it used to establish a theological bureaucracy, and serve as patrons for arts and education. It did a poor to mediocre job of it.
However, roman pantheism lacked the same unifying structure. Roman religion was decentralized, and un-bureaucratic. More often than not its priests were extensions of the aristocracy. This is not necessarily a bad thing. However, when the roman state collapses politically and economically, who will provide the patronage to maintain the scholarly class? Certain centers of trade, knowledge, and learning which withered in OTL might survive, and vice versa, but what factor is there to keep them linked?
Hence, to restate my thesis, for all of its ills, Christianity had a positive role to serve in the Dark Ages as a centralizing agent.