This is a pretty recurring theme; whether you can go outside the Board guidelines and rules.
I'm a pragmatist, and I say that if your teacher says that you can go over the word limit, you can. Unless they're new, misinformed, or not marking the paper, I would stick to what they say. If they're new, or not marking the paper, go see the head of history or your tutor or something. Basically, do what's right for you. Why not confirm it with him in private - if you explicitly confirm that your word-count is fine, you should be safe.
Say you wrote 2500 and were marked down, you could lodge an appeal, but what's the point? The HSC, whilst about learning and improving yourself, is a game that needs to be played well. Jumping through the hoops to get marks can seem silly, but what other option is there?
I'm glad you have a conscience, but remember that this is an internal assesment (albeit one heavily described by the Board) - you're competing against your classmates.
However, I think that your teacher is a poor supervisor to say that 2500 words cannot do justice to your topic. The correct thing to do would be to be a word-count Nazi and get you to focus your topic into something more managable in 2500 words. Any topic can be explored in 2500 words - the scope of the question just needs to be correct.
Worth noting is another idea: That your teacher is actually giving everybody the trial by word-count. Essentially, an early undergraduate or late HSC student can write about 2500 words in a day/night. 5500 words is huge, and, if well-written, forms a pretty convincing piece of evidence that you didn't do the essay at the last minute. Perhaps your teacher is daunted and figures that marking based on word counts is the way to go?
Either way, your teacher could be in the wrong... Just protect your marks like the hydra and his fleece and you should be fine!
