I'm interested to see what other ideas are posted here, but to get things rolling, I'll mention the command line program dd. This utility makes a bit-by-bit copy of the partition, not caring what any of those bits mean. Therefore, it should be adequate to clone an encrypted (or any other) partition.
Time for disclaimer: I have not used Clonezilla, but I just did a quick Internet search to see what it does. The difference between dd and what I think you are used to Clonezilla doing, is that Clonezilla will normally interpret the filesystem and only save the sectors that are used. With dd, all sectors will be saved. So your image will be larger than you are probably used to. My quick search suggested that Clonezilla will use dd if it doesn't understand the file system. So you may already have this option available to you w/o needing to learn a command line interface.
I await to see what other solutions might be suggested.
Last edited by blackhole54; 08-17-2007 at 03:45 AM.
Reason: Spelling correction