When indexing from command line, Ctrl-C and kill -SIGTERM is the right way of stopping Alkaline. If Alkaline responds to search queries, use the AlkalineStop.pl script that is distributed with the AlkalineTools package or use the Shutdown Server command from the online administration.
You should be using kill -9 to stop Alkaline only if you know it is not writing an index (when running with --noreindex , etc). If you fail to do so, Alkaline may corrupt them. If you Ctrl-C or kill -SIGTERM a running Alkaline process, the signal will be ignored when Alkaline is writing indexes.