You can start mission packs with AppleScript.
Open the ScriptEditor located at the "AppleScript" folder inside your "Applications" folder.
Create a new script with the following three lines:
tell application "Quake"
run params "-hipnotic"
end tell
Replace "-hipnotic" with "-rogue" if you want to use Mission Pack 2. If you want to use GLQuake instead of Quake replace "Quake" with "GLQuake".
Save the new AppleScript as "Application".
Open the ScriptEditor located at the "AppleScript" folder inside your "Applications" folder.
Create a new script with the following three lines:
tell application "Quake"
run params "-game MOD_NAME"
end tell
Replace "MOD_NAME" with the name of the mod. If you want to use GLQuake instead of Quake replace "Quake" with "GLQuake".
Save the new AppleScript as "Application".