In classical Physics, it is the theory of waves and the wave equation that has a principle of superposition, not Newton's second law as you are wondering about.
Why Newton's second law is irrelevant: In fact, it isn't linear in gravity: the Force law is $1\over r^2$ which leads to non-linear behaviour. The principle of superposition in QM says something totally different than adding forces as you are asking, it says that if a system can be in state $v$ or it could be in state $w$, then it is also possible for it to be in the state $2v+3w$. This links up to Antillar's answer: the principle of superposition says that the possible states form a vector space. But the positions of the planets in Newtonian graviation, or in Einstein's theory either, do not form a vector space.
But this principle does come from classical Physics, it comes from wave motion: the equation of a vibrating string, $$ -{\partial^2 f\over \partial x^2} = {\partial^2 f\over \partial t^2}$$
for the height $f$ of a string above the $x$-axis above the point $x$ at the time $t$. This equation is a linear equation: the set of solutions is a vector space: if $f$ is one solution and $g$ is another, then $2f+3g$ is also another possible solution.
But this wave situation is much more special than Newton's Law, although Newton's Law is used in proving the wave equation. So the principle of superposition cannot be deduced from Newton's law at all. It is now thought to be a universal principle which is exactly true, even though now QM kind of abandons Newton's Laws, the principle of superposition is now even more important than it ever was in classical Physics. (In classical Physics it was not universal.)
(I suppose one could worry about whether General Relativity's being non-linear means that eventually we will have to modify the principle of superposition.)