Hi Lee,
In England and Wales word of mouth is as legaly binding as a written contract - however in your case it is an statement and proving this would be a pain. Legaly you can challenge this in a cout of law - but then again you might end up paying more for a sol's fee than you would have to pay back.
I would ask them to provide you of proof of overpayment and also ask them why you were informed that it was a tax rebate (misrepresentation of information / incorrect information) and also ask to see your PAYE slips for tax rebates that your emp would have filed, if any. If all else fails arrange a re-payment plan with them - but whatever you do please make sure you put it in writing - otherwise it is their word against yours.
Also on your IR returns for 05/06 you would have declared that �3000 as a tax rebate because that should be tax exempt as far as I am aware so that would support your argument as well.
I would have a word with a legal advisor as well just to prepare for the unforseen!!!
Hope this helps