I use TrueCrypt and Macrium, and I have done both ways successfully. Everything worked as expected.
As you've already figured out, when backing up the (encrypted and running) Windows system, you end up with an unencrypted image - but you can let Macrium re-encrypt it using its own (non-TC) encryption (registered version only). Restoring it will undo the Truecrypt encryption though and you'll have to re-encrypt it from scratch. But TC has no problem with an encrypted system partition that, from its own point of view, was "suddenly and unexpectedly" decrypted.
Quite cleverly, you can save your Macrium backups on an external storage device that's also
encrypted with TrueCrypt, this way you don't need Macrium's own encryption. (You will need to run TrueCrypt from the WinPE rescue disc however in order to mount the encrypted volume on the external storage before you can access the backup and restore it. I do this by running Truecrypt from an USB stick after I've booted the rescue disc.)
I've also done a full sector-by-sector clone of my encrypted system using the WinPE rescue disk (since it allows you to both back up and restore). When I later restored this clone image and rebooted, it fired right up without any problem and the Truecrypt encryption was completely intact.
So, I can vouch that both ways of doing this are safe and work well.