I see two possibilities of resolving specific courtyard problems.
One way is to ignore specific courtyard violations. You can right click on any violation in the DRC window, and then click on Exclude this Violation in the popup menu:
Another way is to edit a footprint and then simply delete the courtyard from it. To do this, just hover over footprint in the PCB and then:
- Press [Ctrl + e] to load it in the footprint editor.
- Remove the lines from the courtyard layer.
- Close the footprint editor.
- KiCad asks you if it should save the changes in the PCB, confirm this by clicking on Save.
If you want to do this for multiple footprints, then also:
- Save your modified footprint in a project specific library.
- Update the schematic to use the footprint links to that new library for every footprint you want to change.
- Schematic Editor / Tools / Update PCB from Schematic [F8]