I'm also not qualified to discuss philosophy or theology, but that won't stop me, so that is what I will do. The only prerequisite to discussing those subjects is a knowledge of your ignorance. Or an unbounded arrogance. I get confused sometimes. Either one works.
Apparently, some atheist web-logs are commenting on how this is a victory for Science over Religion. I was not aware of any church making any predictions about the Standard Model, but I haven't followed what Brother Guy Consolmagno has been up to lately. When one commenter on a discussion site was asked why those atheists are heralding this as a victory over religion, he said without irony:
It is a victory because as science and society advances further and further, less and less of the bible become relavent.[Sic] as necessary.
It is also a victory in displaying that the scientific process works, a concept a vast number of christians dont understand.
I am sure there are several other reasons, but my education and understanding of the particle isnt terribly high.
I am not going to pick this apart because, in all charity, it does describe a lot of the people this person may run into.
This, however, does illustrate one of the many reasons traditional Christianity is a much better intellectual bet than modern "roll-your-own" Christianities. Orthodoxy, Catholicism, and even the magisterial forms of Protestantism have a centuries-long philosophical tradition which is historically engaged with the philosophy of science and they do not have intrinsically unreasonable positions. Whether they are right or wrong, sure, is up for debate in the world, but their current intellectual tradition is going to be at least respectable.
However, non-traditional or anti-traditional Protestantisms run into a problem immediately: many of them are intrinsically anti-philosophical because of the manner in which they reject tradition. Further, their fragmented nature and small population mean that any one group is not likely to develop internally somebody capable of articulating a coherent philosophy of science which integrates with Christian theology (nor are they necessarily going to see why they need to do this). Unfortunately, philosophy is best done by trained professionals, because otherwise you are stuck reinventing the wheel (see: Ayn Rand). Theology, too, for that matter (see: Joseph Smith).
One common trap is a God-of-the-gaps: God's action in the world is relegated to areas where there is current scientific uncertainty. Unfortunately, as scientific discoveries are made, this god's powers get whittled down. The leap to not requiring a god, of course, is natural. Our uneducated atheist friend above directly alludes to this phenomenon. An Orthodox shouldn't have a problem here, but a religion with no exposure to philosophy might easily back itself into this corner. An individual Orthodox believer might believe wrongly on this point, but Orthodoxy as a whole wouldn't. We stand on the shoulders of giants, or at least acknowledge giants and try to stand near them. However, in many of these small religions, they don't believe in giants and every individual is thrown out of the street, essentially, if it's not a matter specifically addressed in their founding documents (sometimes it is, invariably with a form of populist anti-scientism, alas).
In short, it's pretty obvious that a religion with hundreds of millions of adherents across all strata of society and a two thousand year history of philosophy might fare a little better when "attacked" by scientism than an (usually) anti-philosophical 20-60 year old religion with thousands, or perhaps millions, of adherents, possibly self-selected from less educated demographics.