As long as you do it before the kraeusen is very active then you can probably do as much stirring, aerating, shaking or anything else you wish to do to your wort/beer that doesn't also contaminate it.
I quite frequently even agitate my beer after the kraeusen by moving the FV to swirl the beer inside the FV to remove leftover foam and crud sticking to the side above the beer surface level. But only when it's remained sealed up and I'm reasonably sure the headspace is CO2. If I ever break that seal, then I'm careful to not cause movement of the beer any more than it takes to transfer for bottling.