Mathusalem is not intended to clone an entire volume: it's not Time Machine. Mathusalem is only intended to backup to a remote destination a subset of your disk representing your most important data like your documents, email and photos.

Version 1.2 indeed has an issue in which it wasn't checking for free space on disk before starting the backup (this only affected users trying to backup very large amounts of data): this is fixed in 1.3.