Here's a somewhat sketchy proof. It's topological rather than graph-theoretical.
Start with a projection $p: S^1 \rightarrow S^2$, an immersed circle in general position. $S^2 - p(S^1)$ is a collection $R$ of regions $\{R_i\}$. Color them like a checkerboard, as follows. For any $R_i$, the winding number of $p$ around $x \in R_i$ does not depend on the choice of $x$. So we have a map $w: R \rightarrow \mathbb{Z}$. Color the regions white or black depending on whether $w$ is even or odd. Now every edge of the embedded graph $p(S^1)$ has a black region on one side and a white region on the other side.
So the colors alternate around each vertex of the graph. Each edge of the graph belongs to the closure of exactly one black region. Also, each vertex has degree 4, and each region is an open disk.
Now assign a value to each end of each edge with the following rule: traveling clockwise around the inside boundary of a black region, as we travel along an edge, mark the beginning "over" and the end "under". It's easy to check that this assigns crossings consistently to the diagram: at each vertex of the graph, four ends of edges meet, with two opposite ones marked "over" and the other two marked "under". Also, it's clear that the crossings alternate.
So this is the set of crossings you got by simply alternating crossings (up to swapping over and under), and it's consistent.