i think they concluded the holes were sockets for stones for a number of reasons - one of which is because of the amount of chippings of Bluestone they found in the area, and another being that holes which have had stones in them have a variety of archaeological evidence to support such a conclusion, including the way the earth is packed, the way the hole is cut, and whether there's evidence for packing stones, etc, having been used to hold the stones in place.
the combination of this kind of evidence plus the lack of evidence needed to support the hypothesis of wooden posts being in the holes (organic material would likely be left if wooden posts had been in the sockets) is generally how archaeologists draw their conclusions -- it's become quite a science over the years, and, as time passes, technological advances combined with a greater understanding gathered from other excavations/investigations allows them to build a better picture.
they have found sites with sockets which they believe held wooden posts - so it's not as if they discount such a possibility outright, such things do indeed exist (see Woodhenge for example - but there are plenty of other sites which feature 'post holes', although not usually in large circular arrangements such as discovered at Woodhenge)
of course none of these conclusions/hypotheses can be proven as totally and absolutely 100% accurate, and it is often the case that archaeologists will draw new conclusions in later years, as technology improves and more information is gathered from other digs - which is exactly what they've been doing with these recent excavations in the Stonehenge area.
personally, i'm of the opinion that if they say they don't think it was wooden posts but it was stones, then they're likely right - they are experts after all, and they don't really just make this stuff up, it's based upon the evidence at hand at the site and the culmination of years of study and research across many similar sites.
(in some ways it's like if i repair a pc, and tell my customer that i think it's a hard-disk failure - i've based my decision upon years of experience and the evidence at hand - in such a situation, ie. being the repair-man, i am the 'expert' in that equation - of course, Joe Public may say 'how do you know? it could be the motherboard or the power-supply or something' - and sure, it could be open to interpretation and later discoveries of related information, but i'm likely to be right)