Perhaps i didn't read it right; does malleability cause any issues in the real world for anyone that only deals with confirmed transactions?
Potentially.
https://bitcointalk.org/index.php?topic=460944.0The two issues that would face a user using a stock client would be incorrect reporting of duplicate tx and problems with spending unconfirmed change output. Both are described in the linked thread.
There are pull requests to provide better handling of both issues and eventually they will be included in the mainline client. These "fixes" don't make tx id immutable (that will require a protocol enhancement) but they will cause wallets to behave in a more expected manner when they encounter duplicate transactions. The long term solution is to make tx ids immutable (or at least immutable by third party) but that will take a lot longer as it may require a hard fork.