Am I the only paranoid person here?
Yes, I'm afraid I think you are. This technique of using out-of-band audio signals to carry small amounts of digital information is, with due respect to the OP, laughably simple to do and has been used by the world's telephone systems for years. It's how payphones know how many coins to require for a given call. No doubt dozens of other examples exist too.
There is information out there which, it could be argued, has no legitimate purpose and should perhaps be monitored or restricted... information like "if you mix chemicals A, B and C in these proportions then they'll go bang", perhaps. But techniques for things like communication, timing and security are so widespread, have such obvious and useful legitimate purposes, and are so readily derived by anyone with some basic electronics knowledge, that to try and control them would be utterly ridiculous.
To the OP: I'd start by synthesizing a swept sine wave tone and analysing what comes out of your sound card, to find the highest frequency it will produce at a usable amplitude before the output filter cuts in. That's the frequency to modulate to carry your signalling.
Then I'd build a high pass (analogue) filter - maybe a 4th order VCVS type based on op-amps - to filter out everything below this frequency, and use a peak detector circuit (diode + capacitor) to measure the peak level of the resulting signal. Feed the output of this into your microcontroller, and all you need to do is pick a suitable threshold level to determine whether the signal you're after is present or absent. Then you have a serial bit stream which you can decode; you might even be able to use a UART.