Is this "transaction malleability" really an issue?
Here's a good interview by Gregory Maxwell himself who's a Bitcoin developer: 


  Oh there is a “problem” in the Bitcoin protocol, known since at least
  2011 (see the link I gave). But for normal applications, not involving
  unconfirmed transactions, it shouldn’t cause any severe problems
  because wallets can handle it locally.


This has to do with systems, such as Mt.Gox, that rely on unconfirmed transactions. Normal Bitcoin apps don't rely on unconfirmed transactions.

The Transaction Malleability issue that Mt.Gox talks about has been around since 2011. It only effects transactions which are not included in a block. Once a block is hashed, you can't change the transactions within it because then the hash of the block would have to change as well.

For all other Bitcoin applications that rely on confirmed transactions, as they should, this is not an issue.