The simple solution given by Jonathan works with a modification to cheat Pandoc. Instead of direct Latex commands such as
\begin{center}
Text
\end{center}
you can define your own commands in the YAML header:
header-includes:
- \newcommand{\bcenter}{\begin{center}}
- \newcommand{\ecenter}{\end{center}}
And then you use:
\bcenter
Text and more
\ecenter
This works for me for centering a whole document with many code chunks and markdown commands in between.