Generally, I find tkz-berge is useful for doing standard graphs quickly in a pinch, but if I need to deviate from a standard graph, it's usually faster to break out plain TikZ and write it from scratch. That's what I've done in the example below.
A tkz guru may be able to colour the vertices differently with ease, but I found this method easier (and fairly simple).
Here's what it looks like:

and here's the associated code:
\documentclass{article}
\usepackage{tkz-berge}
\begin{document}
% Draw a cycle of vertices
\newcommand*{\drawvertices}[7]{
\foreach \t/\mycolor in {1/#1, 2/#2, 3/#3, 4/#4, 5/#5} {
\begin{scope}[rotate = \t * 72, xshift=#6,
VertexStyle/.append style = {ball color = \mycolor}]
\Vertex{#7\t}
\end{scope}
}
}
% Inner 5-cycle
\newcommand*{\innervertices}[5]{
\drawvertices{#1}{#2}{#3}{#4}{#5}{\RA}{a}
}
% Outer 5-cycle
\newcommand*{\outervertices}[5]{
\drawvertices{#1}{#2}{#3}{#4}{#5}{\RB}{b}
}
% The star-like edges in the inner cycle
\newcommand*{\staredges}[5]{
\foreach \u/\v/\edgecolor in {1/3/#1, 3/5/#2, 5/2/#3, 2/4/#4, 4/1/#5} {
\tikzstyle{EdgeStyle} = [color = \edgecolor]
\Edges(a\u, a\v)
}
}
% The outermost edges
\newcommand*{\outeredges}[5]{
\foreach \u/\v/\edgecolor in {1/2/#1, 2/3/#2, 3/4/#3, 4/5/#4, 5/1/#5} {
\tikzstyle{EdgeStyle} = [color = \edgecolor]
\Edges(b\u, b\v)
}
}
% The edges that join the inner and the outer five cycle
\newcommand*{\betweenedges}[5]{
\foreach \u/\edgecolor in {1/#1, 2/#2, 3/#3, 4/#4, 5/#5} {
\tikzstyle{EdgeStyle} = [color = \edgecolor]
\Edges(a\u, b\u)
}
}
\begin{tikzpicture}[rotate=90]
\GraphInit[vstyle=Art]
% Set the inner and outer radius as with \grPetersen
\newcommand*{\RA}{2.4cm}
\newcommand*{\RB}{5cm}
\innervertices{green}{red}{orange}{yellow}{blue}
\outervertices{purple}{cyan}{magenta}{lime}{pink}
\staredges{red}{orange}{green}{blue}{pink}
\outeredges{green}{blue}{purple}{cyan}{yellow}
\betweenedges{blue}{pink}{cyan}{teal}{yellow}
% Get numbered labels (like in the picture)
% \foreach \number in {1,...,5} {
% \begin{scope}[rotate = \number * 72, xshift=\RB+0.8cm]
% \draw (0,0) node {\LARGE{$\number$}};
% \end{scope}
% }
\end{tikzpicture}
\end{document}
What you change
You need to set \RA and \RB to the inner/outer radii that you want; there are analogous to the parameters RA and RB in \grPetersen.
In each of the commands from \innervertices{} to \betweenedges{}, change the colours for those that you'd like. Each time, you start at the vertex or edge incident with 1, and head counter-clockwise. (Look at the picture if it helps.)
The colors are defined by xcolor. You can find a list of the standard colors on page 17 of the package documentation, or find out how to define your own colours in the same document.
I set up vertices just as you do in tkz-berge normally: with a \Vertex command, and they're moved to the appropriate position with a scope. These are then joined with the tkz-berge command \Edges().