It's too difficult for us on the outside (and maybe even some of the 343 engineers themselves) to tell whether or not using the PC ports made the release better or worse. Are the PC ports worse than the original Xbox versions? Sure, but perhaps the architecture of the PC ports were such that they allowed much easier integration into MCC (which is what I suspect). Maybe they saved time using the PC ports, and the time they would have spent integrating the original versions would have given them less time to work on stability and made the launch even worse.
I don't know of course, just spitballing. Now that 343 has made things way better, I imagine that there's no going back. Trying to start fresh with the Xbox versions would probably result in ungodly amounts of lost work that has to be redone, and for every one thing it does better, would probably make 10 other things worse. My understanding of their current approach is that they're trying to get the existing MCC versions of the various engines close to the Xbox versions. I think that's the right approach. Imitate and reimplement until you reach something approaching parity with the originals, and 95% of the players will be 95% happy, which is a win.