As long as the works are promulgated by a NOTAM with any reduced runway lengths and information about taxiway closures etc, it shouldn’t be a problem.
Not sure why CASA would need to get involved, however this is Australia......
As far as Part 139 and RPT ops go, the onus should be on the AOC holder to decide whether it’s suitable to continue to operate into an aerodrome that’s undergoing maintenance/upgrade, not CASA or the Part 139 holder.