In FFXIV config if you hit General then Sounds, theres a checkbox that says Disable Sound Device which will prevent ffxiv using the sound card which completly mutes it, the downside is if you want sounds in cutscenes you have to exit the game before the mission, but for now atleast it works for preventing those anoyying sounds.

This only stops ffxiv using the sound card, you can still listen to music, talk on vent/TS/Skype while playing, its the only way I have found to solve the problem