vmkfstools is a good utility - it converts from one format to another. What format are the EC2 disks? I imagine they're probably raw, which should work just fine - vmkfstools ought to be able to pull those in and make them vmdk files. On the Linux side there's also the qemu-img tool from the Qemu package that does various file format creation and conversion, and has some support for VMDK files.
Maybe it's possible to use some kind of image tool, like ghost to clone the instance, and then restore it inside an already created VMDK.