No, all bacteria would not be killed, but most will – quite enough that you are unlikely to be severely infected/affected, even if the only bacteria left are MSRA. Remember, as is being said already here, your body has defences against bacteria. The more you are exposed to bacteria, especially when young, the more your body will make antibodies (the defences) that will fight against future exposure to the bugs.
It is being found that children brought up in highly clean environments do not build up antibodies well, and so are less able to defeat infections that they come across. Grubbing around in the mud is good.
Obviously, putting muddy hands in your mouth is not a good idea, in my experience, because you are likely to pick up worms. Eating food that has gone off is not wise; not washing your hands (with soap and water) after the lavatory (toilet) is bad. That way, you can infect yourself with bacteria that live in your gut (like e. coli), which are safe there, but that can make you very sick if they are eaten.
Remember that soap is a natural bactericide, so hand washing kills the most annoying bacteria. But you do not need to be neurotic about things unless you know that you have been handling something that can pass bad infections to you – animals, birds, raw meat/fish.
In the end, remember what you were taught as a child/teenager – wash your hands after the toilet, before eating, after being outside, when you have a cold or are in contact with an ill person.