System Ninja is an alternative. But keep in mind that it is more aggressive in cleaning up. While I myself have not experienced any troubles with it, others have. Or, at least they claim to have.
Then again, I must add that 90% of all the tools that I use are "portable". Most of the tools that do not have such a mode as an option, can either be gotten from sites such as portableapps.com or winpenpack. and if you strike out there, you can use a tool like 'Cameo' to create a (semi-)portable version of the tool.
CCleaner won't be able to affect the workings of such applications and the same is true for System Ninja. All of the above is mentioned just to clarify that results may vary on your system.
At least it is still nice to read that companies still listen to the reactions of their users.