As long as the workaround was known, well... I don't know exactly what the military procedures are for situations like that, but updating an active rocket defence system in area where you don't necessarily have trained engineers -vs- rebooting it every day or so to make sure it works. It looks like a simple choice to me.

Also looking at who actually makes the mistake - if someone gives you an update and the system fails, they're at fault. If you give clear instructions for operation and users don't follow it...

According to Wikipedia, the workaround came from the Israeli army, who found the bug, not the manufacturer. The instructions for this workaround did not propogate clearly and thus weren't followed.

Being defenseless for a few minutes every day during a reboot hardly seems like a reasonable fix anyway, especially if it becomes standard procedure that your enemy may learn about.

The fact that the manufacturer did release a patch, rather than a workaround, the day after the accident suggests that this was indeed the safest course of action. It was just taken too late.