There is not enough information given about the project to be able to advise on a good solution.
It seems that an interrupt would be the best way to generate the clock.
For a 20us clock cycle, PA6 would have to be toggled every 10 us. This would correspond to once every 18 system clock cycles, so, there are tight time restraints.
It is not know whether interrupts are being used for any other functions.
The slow system clock places limits on the microprocessor's capabilities.
Timers and USARTs can use external clock inputs other than the system clock, if this is an option.