This leaves me with some questions:
1. How long will it take for a new reference client version to make a real impact on the network?
2. What software do miners use? If they use other software how long will it take for that to be updated? Attackers could still try to plant mallified transactions by peering with miners using older software right?
3. What is to stop an attacker to hire his own mining equipment and stick mallified transactions in it? Or is this too expensive?
As far as 1) There's no impact from the problem as it is, it's just nerves.
As far as the rest, the blockchain stops all that already, this is only a problem for exchanges that process withdrawals before confirmation, which you would think would be none of them.