https://youtrack.jetbrains.com/issue/IDEABKL-6449
Since IntelliJ evaluates the environment variable LC_TIME according to DateFormatUtil.java, setting LC_TIME=sv_SE.UTF-8 brings the ISO-8601 format to IntelliJ. I also had to set LC_ALL, e.g., to $LANG (en_GB.UTF-8).
Make sure to first comment out the string sv_SE.UTF-8 in /etc/locale.gen (as root) and to rebuild the locales by running locale-gen (as root).
Update 2020: IntelliJ supports customizing the date format in the preferences: