It turns out the game will indeed crash if you have a custom entity (one not listed in entities.txt) which has been killed and you try to save the map. To avoid this, you'll need to either: (1) add your entities to entities.txt with unique ID numbers, with the drawback mentioned earlier that users will have to make the same changes to their own copies of entities.txt; or (2) make sure you don't save in the scene editor when there's any chance a custom entity may have been killed (this includes autosave, which can potentially strike at any time).
In theory, you could edit the map XML files to replace your custom entity IDs with entity names, to avoid the drawback associated with the entities.txt method. You'd need to parse the j="" attribute of the <Entities> tag, and replace each occurrence of your custom entity's ID (e.g. "1234") with a -1 and the entity name (e.g. "-1 MyEntity"). If you do this, be careful you don't accidentally change other entity data which just happens to have the same value as the entity ID!
Shameless self-promotion: While this requires a bit of technical knowledge, you could also compile
my modified source code, to which I've just committed a fix for this bug. Unfortunately, there are incompatibilities in the script interface that prevent scripts written for the Humble Bundle (1.1.3) and earlier releases from working on the modified source code, and vice versa; see
this mailing list post for more information. Alternatively, you can build from the "custom-entity-crash-fix" branch to get
just this fix and remain compatible with the original script interface.