I agree that if the write-ins are being counted based on “intent” then any write-ins for Miller should certainly count. I just have not seen any article with any numbers about whether there were any such write-ins or not.
I can even see why somebody would write-in Joe Miller. After all, the write-in ballots will all be visually inspected, whereas machine counted ballots might have their counts diddled with. Or ... some voters might have thought it would be cute for Murkowski to think all the write-ins must be for her, only to be embarrassed during the actual counting.
I think some people just got confused with the write in stuff.