Along the way to a much simpler solution to a homology problem, I thought about computing the fundamental group of $S^2 / A$. I quickly ran into trouble, so I want to know if there is there a slick way to do this. (For nontrivial |A|, of course.)
I don't think that Van Kampen's theorem works, since the intersection will not be path connected for $|A| \geq 2$. (At least for the obvious covers.)
Let us do first the following simple computation. Let $D$ be the closed unit disc in the plane and let $A$ be a finite subset of the interior of $D$. What is $\pi_1(D/A)$?
Let $n=|A|$. It does not matter which $n$ points are in $A$, only the cardinal of the set, so we may assume that the points of $A$ are the $n$ vertices of a regular polygon centerd at the origin. Let us take basepoint in $D/A$ to be the (image of) the origin. There is an obvious retract of the space $D/A$ to the space obtaned from a regular $n$-gon by identifing its vertices. This looks like a parachute.
This space can clearly be constructed as a CW-complex as follows: start with one vertex. Next add $n$ $1$-cells in the form of loops, and now glue a $2$-cell in the obvious way. The fundamental group of this space is then $\langle x_1,\dots,x_n:x_1\cdots x_n=1\rangle$. This is easily seen to be a free group in $n-1$ generators.
Now your sphere can be covered with two open sets. One of which is an open disc and the other an open set which deformation retracts to my $D/A$. The intersection is a (thick) circle. Now use van Kampen.