I haven't checked all this myself [thanks heaven for monthly billing] but I would imagine that they cannot unissue an invoce in many countries. They have to issue a refund instead, otherwise people could use the invoices for money laundering... (long and twisted logic that I won't go into now).
If the refund is only 50% of what you envisaged, then I would do one of two things:
1) Try to get them to give you the other half back as well or 2) Tell your credit card company that the transaction that was clearly not relevent is not infact due as the service was not delivered. then let Microsoft fight with the credit card company.