Added config option "fill-memory-tolerance" which defaults to 500. If/when the Fill process pauses due to low memory (<200 MB), this setting is the amount of free memory (in MB) required to be available before it automatically continues.
This option isn't made available to change through a command as most people shouldn't change it. It's been made available for people who are running extremely low memory (and thus necessarily tiny) servers which have less than 768 MB memory available to their CraftBukkit server.