I was wrong blaming upstart for non-stopping timenow.conf, it's not it's fault.
When it starts timenow.conf, it actually starts su, which starts run-standalone-sh, which starts timenowd.
There are two problems:
1. busybox-power (su is busybox) doesn't send SIGHUP to it's child processes sometimes (in this case it doesn't). So, if you have busybox-power installed, when you stop timenow.conf, upstart kills su, but run-standalone.sh and timenowd keep running.
2. Your program does not die when it receive SUGHUP. So, even if you haven't busybox-power installed, when you stop timenowd.conf, upstart kills su, which kills run-standalone.sh, which kills timenowd, but it ignores that and keeps running.