A good deed is a good deed regardless of the motive. The drowning kid in your example just wants to not be drowning any more, he doesn't care why you're pulling him out of the water.
Motivation has more to do with what you get out of your good deed. I mean what you get out of it mentally. If you do the good deed for greed (for example), the outcome could be positive or negative depending on whether you get rewarded. If you do the deed simply for the sake of doing good, however, you are always rewarded. Even if the outcome isn't what you hoped for, you can take a great deal of comfort in the fact that you were doing what you deemed to be the right thing.
I am decidedly agnostic, but as far as that part of your question is concerned, I would imagine God to be purely concerned with motive.
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"If I cannot smoke cigars in heaven, I shall not go!"
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