It makes sense to me. The 5 am hour has generally been reserved, whenever possible, for shows that can segue back into the younger audience of regular Cartoon Network when it starts at 6. It doesn't always work out that way for one reason or another, but when they can, that's usually what they aim for. That's why Inuyasha is there now, because IY always had a pretty young skewing audience. Clone Wars fits in that graveyard slot just fine, too. In fact, I'd almost consider putting Inuyasha at 5 and Clone Wars at 5:30. I assume the only reason they're not is simply due to the ages of the shows.
Clone Wars was also pretty disruptive to the general flow of the block in the slot that it was in. It's a big stylistic and tonal shift smack in the middle of the lineup. Makes more sense to switch that out than one of the more established shows like FMA and GITS.
