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Whenever I play audio using the built-in analogue output jack, I lose control of GPIO 4 pin.

Specifically, I am transmitting FM waves by Pin 7 using pifm (http://www.icrobotics.co.uk/wiki/index.php/Turning_the_Raspberry_Pi_Into_an_FM_Transmitter). But whenever I play audio when doing so (by "aplay input.wav" command) the fm transmission stops.

Is there any workaround that would let me use both audio playback and CLOCK output on pin 7 at the same time?

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I don't think so.

Audio through the sound jack uses the PWM peripheral (Broadcom's choice of name). This conflicts with PiFm which also uses the PWM peripheral and configures it differently.

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