As a professional conference producer I agree that the audio tools in PowerPoint are non existant. If I needed to run audio during a PPT presentation, I would generally route the audio through a sound mixer so I can fade it when I want!
You're in a difficult position though. So, if you can estimate how long you need the clip to be, then the easiest way of dealing with the issue is to run the clip through a sound editor (there's usually one provided with your sound card) adding a fade at the appropriate point and then resaving the file.
Awkward, but not impossible!