According to the Linux Libertine font tester you can have Greek small caps.
However the following example does not yield the desirable result:
\documentclass{article}
\usepackage{fontspec}
\setmainfont{Linux Libertine O}
\begin{document}
\textsc{Small Capitals}
\textsc{Πεζά κεφαλαία}
\end{document}
Output:


