I'm really not quite sure what the problem is your referencing and, to be honest, I wonder if you're suffering from a case of "A little knowledge...". Hard drives do accumulate dead data, but it's unlikely to be of any concern whatsoever while the file system is doing its job. Even less on on an SSD where seek times are essentially null.
Anyway, what you're after is pretty much the default anyway - you simply want a piece of software which does a file system aware file and partition copy - rather than a bit for bit forensic copy. The latter takes MUCH MUCH longer and so is rarely the standard.
CloneZilla should do what you need, but so should any consumer off the shelf cloning software.