Thrall is a Frostwolf, of course he's wearing blue. This being some hint towards the Alliance is just the same hyperbole that made people think Saurfang was going to join the Alliance and the Alliance armoured Frostwolf was some kind of hint ^^
Now if you count 'blue' as being a hint towards being more on the 'peaceful' and 'balance' side and 'red' more the 'fierce' and 'warlike' side, you may have a point that even fits with the elements that represent those things.