I would suggest that the getting knocked over part is simply you mishandling the waves. Naturally, with the rudder down vs. the rudder up, the kayak behaved a little differently. You were able to handle one behavior a bit better than the other for whatever reason. But I would suggest you look at what you did with your body, kayak, and paddle, and work that out so that it doesn't matter whether your rudder is used or not in terms of capsizing.
Once you get that figured out, then you can start experimenting with whether or not you prefer your rudder deployed in different situations. But the idea that you can and can't stay upright in waves, or that you can or can't handle your kayak in waves, and that it might have to do with rudder deployment, just doesn't strike me as a good focus.
Any reason you would be more likely to capsize? With a skeg or rudder deployed, the kayak has a better hold on the water, and is less likely to skid, for better or worse. If you're not in particularly solid command of your kayak, and you're used to the bottom skidding sideways to a degree in front of the wave, and you deploy something to hold the kayak more static in the water, I can see where it could cause you to tip over. More appropriate and comfortable edging and/or leaning, and fluid bracing ability, should prevent you from living that uneasy on the edge of balance.
Bent Shaft Canoe Paddles
YakCatcher Rod Holder
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