It is a result of Tamagawa that for two affine curves $C_1, C_2$ over finite fields $k_1,k_2$ any continuous $\pi_1(C_1)\rightarrow \pi_1(C_2)$ arises from an isomorphism of schemes $C_1\rightarrow C_2$. Hence, if $\pi_1( \mathbb{P}^1\setminus\{a_1,\ldots, a_r\})$ were independent of the choice of the $a_i$, then the isomorphism class of the schemes $\mathbb{P}^1\setminus\{a_1,\ldots, a_r\}$ would be independent of the choice of $a_1,\ldots,a_r$.
Tamagawas is Theorem 0.6 in this paper:
The Grothendieck conjecture for affine curves, A Tamagawa - Compositio Mathematica, 1997 http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=298922