Answer by arminb for Can i use different timer channels when other channels (of the same timer) have i2c alternate function

The PWM and the I2C module are connected to the GPIO output via an multiplexer. By configuring related registers in your microcontroller you can decide which output will be passed through to the GPIO. This block diagram shows a very simplified overview of the relations between peripheral modules, multiplexer and output:

By setting SEL to 0or 1 either IN0 or IN1 will be passed through to the GPIO pin.

So the answer is: No, your setting for the PWM frequency will not have any impacts on I2C behaviour.