Malleability could also happen without bad intention, but the refund tx is only needed if the normal trade does not get completed.
In that case both have an incentive to agree to a new refund tx with the changed TxID from the now published Tx1 to get back their payments.
At least Bob has no extortion advantage compared to Alice.
There is still the issue of mutual destruction though. You may ask why that would happen but I can imagine if a decentralized exchange like this really took off it might be worth it for the existing exchanges to mess with users of the decentralized exchange by locking up their funds at random.
But I agree with transaction malleability out there this seems like the only possible solution.