Suricata - disable.conf seems not working

Currently the disables are done, then the enables are done which can revert the disables. Unfortunately there is no way to do what you are trying to do, but it has come up in the past and I have a few ideas.

While pass is an option, note that the modify step happens last. You could add an line to modify.conf to disable this rule as a (slightly non friendly) work-around.