Can you resize the wubi loopback file? That would be my first port of call. Only way I have ever done anything like this safe is create a new loopback file formated with ext3. Yes basically a partition inside a partition. We have made moving wine drive C hard for very good reasons. Until you can do either above moving wine drive C is not safe. Major issue you have is items installed in wine should not be mixed with Windows it is asking for trouble. Also NTFS is not supported enough. Yes there is a limitation on how much support Linux can do on NTFS before it starts breaking windows.
