Yes, like it says in the article we've known this for many years now. I learned it in my intro entomology class two years back. Even more surprising then this....did you know that Siphonoptera (fleas) are actually Mecopterans (scorpionflies)? And to make things even crazier....did you know that the strongest molecular evidence shows that insects arose directly from crustaceans....making insects nothing more than highly modified land crabs...as opposed to being the sister group to Myriapods. What I'm really looking forward to finding out is what Strepsipterans are....beetles or flies (biggest debate in insect phylogenetics at the moment).
The haltere is simply explained by and hox gene reversal. A fairly simple genetic screw up. As for who classifies them as flies, that is the prevailing hypothesis at the moment. All of the molecular evidence supports them being flies, however other researchers argue that this is simply a flaw caused by long branch lengths. (Streps and dips both have incredibly long branch length as compared to all of the other holometabolous orders. Unfortunatley few insect genes have been fully sequence for all of the orders so this could just be the 18-S data set that has so many changes for those two orders.)
As for them being beetles, that comes from them being so morphologically similar and a very similar life cycle to Rhipiphoridae. This is easily explained away by convergent evolution, seeing as how both Rhipiphorids and many Streps are parasites on wasps.
To make matters even worse, there is a Hemipteran family that has a similar life cycle (including a pseudo-pupal stage) and similar morphology to Streps, so they might not even belong in the Holometabola.
As far as Streps go....I've got one specimen in my collection and I don't really intend to find many more. Slide mounting is not fun in my book.