The short answer is that yes, that’s one view of the way the universe works. There is only one timeline, and messing it up means you’ve written yourself out of the universe. (This is the view Back to the Future takes, because it’s much more fun to have The Laws of Physics be an antagonist alongside Biff.)
However, you’re right. It results in a paradox. Instead, let’s assume that the universe isn’t so fixed as to have the One True Timeline. In this case, Marty’s component atoms won’t spontaneously disappear no matter what happens. Think of Marty traveling through time like he’s on a canoe in a river. Marty will float down the river at a set pace for his entire life, or he can paddle back up the river and take a different fork.
Imagine Marty comes to fork ABC in the river, takes path A for a bit, and then litters on the shore. Now, if he paddles back up the river and takes path B or C instead, the litter won’t disappear: he’s already littered. He’s double dipping on the river, not replacing his actions.
If you think of time as a dimension just like length, width, and depth, Marty can travel back up the time stream (in this case, it’s especially odd, because he’s traveling to before he’s even born) freely. But his component atoms have no memory: they don’t “know” that he’s accidentally prevented his parents from marrying. The only thing he can change is what kind of world he returns to in 1985: Marty’s component atoms don’t care whether he’s on path A of a river, path B of a river, the original 1985, the improved 1985, or even 1955. They’ve already been assembled once, and traveling to 1955 is no different to them than traveling to 1986, no matter what happens in 1955.