To be fair, Christianity has a long history of taking 'pagan' and incorporating it. Look no further than the two main religious holidays of Christianity: Christmas and Easter. From the yuletide log to the easter bunny delivering eggs, significant non-relgious idealogy survives in what are considered fundamentally religious holidays. Whether Theodosiuous couldn't find a way to make Christianity part of the Olympics or had some other motive, we'll never know. Perhaps he was less savvy than the missionaries that came before him, or just wanted to show his power as emporer.

@Another Jake
Your article doesn't really argue the fact that Christians killed the games, more that they were justified in doing so, on grounds that could easily be used to end the NFL now. I'm not sure that's a long term answer to a (deserved or not) reputation of intolerance.