Currently, if you receive money it is possible to trace it back to some event, be it a theft, or funds used in some legal or moral grey area.
While these tools will make it easier to launder money, they will remove this "taint".
It is possible and likely that governments will attempt to censor transactions using these "tainted" funds, seriously damaging fungibility.
Many believe that for digital currency to succeed, it must be fungible - the title of the Bitcoin whitepaper is "Bitcoin: A Peer-to-Peer Electronic Cash System".