How to fix SyncMate kernel panic at El Capitan boot
So, for anyone who is in a similar position to me, the critical step that I was missing after getting rid of the offending .kext, was removing the various caches that were resulting in it still getting loaded during the FileVault startup process.

Removing /var/vm/sleep* and /var/folders/* from the FileVault volume caused all the caches to be rebuilt and the system booted correctly.