I got that feeling too. He definately knew of her and was not comfortable about her. Then again the Sisko once punched him, and he did not retaliate as well. In retrospect (ret-cons nicely) he did know who he was boxing with. It could be said he stopped harassing the Prophets' kid because it wasn't as much fun as bullying Q, but maybe it was also a bit of a diplomatic or strategic bad idea.I always assumed that for whatever reason she was somewhat immune from Q's powers and perhaps somehow a danger to him, without having Q-like power herself.
Guinan, there's a lot we don't know about her, and it will be interesting to see if we find out in the next Picard season what the deal was between her and Q, and that gesture.