Wait a long time. You see YOUR transaction as -1, but how do you know the malleated copy has not confirmed? Maybe check a few explorers for that address, to see if any still have transactions in the mempool, or if a payment confirmed with same value confirmed around the same time.
Malleabililty causes transactions to have different txids, so, if your wallet thinks it went out as aaba....., but it confirmed as d4d3... It will mark the first as -1, and deduct from your wallet anyway.
@livte - You are aware allowing 0 confirmation transactions to be spent is totally unsafe? If your product touches customer funds, you'll be inviting either (i) fraud, or (ii) customers wondering why their money isn't going through (iii) or it showing up twice....
Find me one place that says 0-conf is safe.
you can check if the outputs of your original transactions has been spent to the correct recipient.
if thats the case your transaction has been mallated and accepted by a miner...
hopefully this problem goes away fast (afaik as soon as all miners stop acception highS transactions)