"It bugs me that Christians are so unaccepting of alternate versions of what happened."
It doesn't bug me. If I sat down tomorrow and wrote the Gospel according to Mario, it would not become part of the canon. Sometimes, when something gets left out, it is because it is simply inaccurate. More specifically, about Nag Hammadi's Phillip Gospel, I consider it unlikely in the extreme that Jesus was married or messed around with Mary or anyone else. First of all, it was accepted that Rabbi's would be married and therefore, if Jesus were married, there would have been no reason whatsoever to conceal that fact. Second, and much more importantly, the single most significant theme of the New Testament is the marriage between the Messiah and the Ecclesia. You can read the N.T. and never notice it, but once someone points it out, it is like D'OH!
Given the coherence between the 1st century marriage customs and the events in the Gospels, it is clear that Jesus was abiding the law and living out the marriage plan - only NOT to an individual. Had he been breaking law or custom, his enemies would have accused him of those breaches and the accusations would be a matter of record today.
In fact, it is partly because the accusations made against Jesus by his opponents survive in multiple sources, that we can establish so many things about Jesus as facts. (Ernest Martin reveals much of this in his book Secrets of Golgotha, and Jonathan Cahn's tape: Mystery of the Temple Doors also discusses these things: tape number 35 here: http://messianicfellowship.50webs.com/tapelibrary.html
"Faith does not mean I have to close my eyes and believe what others tell me is true."
At some level, that IS what faith is. Just as it is true that science is an effort to discover truth that does NOT depend on human authority for it's veracity. But since you and I cannot afford to perform, for example, the EPR experiment in our basements... in practice... we DO depend on the testimonies of scientists as IF we are "closing our eyes and believing what others are telling us." Sometimes this is safe,�and sometimes it is not. The cool thing about the Star of Bethlehem subject is that it can bring a hard science (Orbital Mechanics) to the table as a means of evaluating the veracity of the Bible. By the way, here is another good link - to the first chapter of Martin's book: http://www.askelm.com/star/star001.htm
This is an instance of a very productive intersection of scripture and (hard) science.