The OP is three months old. Since then there have been two updates to Ccleaner. I am sure the last takes care of Windows 7. I must admit, referring to the OP, that I could not personally see any "dramatic changes "in the structure of the registry,
I do not use a registry cleaner too often, as I don't feel it makes any significant difference to the overall operation of the OS, to remove one or two superfluous entries. I prefer, once in a while, to manually look at the two software items, under Hkey_Current_User and HKEY_Local Machine, and remove any items there, which I have uninstalled but have not been cleaned .
But, on an original install, if the registry is examined, a user will see that Microsoft have been quite lazy and left a heap of Vista items sitting there. At that stage, I have, on countless occasions, run Ccleaner, without mishap. It removes a huge number of entries, without harm to the OS. (It is more than a hundred, but I don't have the exact figure to hand).
But anyone having problems (I would be interested in seeing a post about those. ) should keep in mind that Ccleaner is customisable and does a bit more that clean the registry. Perhaps the problems, if any, lie elsewhere?
See here:
http://www.piriform.com/ccleaner/features