Submission does mean defeat. It's actually a synonym for the word. When you submit you give in which is terrible. Defeat is actually a synonym of submission. Giving in wouldn't be that bad itself if you were giving in to the moment or even into even into a temptation because you can learn from it.
When you submit you pretty much give the person, thing, or whatever you are submitting to power over yourself. Power is not everything when you are dealing with other people, but no one should have power over you. Only you can control you, and you should fight for that. The reason I say submission is defeat is because once you submit you have basically decided to stop fighting. You are fighting everyday until you decide to quit. Once you quit you have been defeated. The easiest thing to do in life is to quit. Submitting would be like taking the easy way out.
In the book Panleux got sick. His symptoms weren't necessarily typical of the plague. Anyway, Panleux didn't even try to fight his illness. He let it take its toll and eventually kill him. He did not go see a doctor or anything like that. Tarrou on the other hand caught the plague and fought it. Yes, he did end up losing the battle, but at least he tried. Tarrou wanted to get better. The plague put up a better fight, but it did not defeat him.
It is possible to accept something with out submitting to it and not being defeated. Submission is defeat, but that doesn't mean go out and rebel. It is possible to accept something you don't like without being defeated. As long as you never loose what you stand for you will never be defeated.