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Hmm. I also studied Latin at school (which immediately dates you) and the classical Latin pronunciation would indeed be Crew-kis. However there are various national traditions of pronouncing Latin, the Germans do it differently from the English. The scientific profession has never been too particular about authenticity of pronunciation of foreign terms and the Americans' (who wrote that website) use of Latin has its own peculiarities. There is a tradition in Australia derived partly from church musical use where a lot of Latin texts are sung to use the Italianate pronunciations which gives the genitive form of crux as crew-chis (similar to what Ken said) and this is what I've always said.
On the other hand I don't often speak astronomical names out loud to others so this could be non standard use. I still have absolutely no idea how to pronounce Bootes.
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