Table \rowcolor \columncolor \multirow and \multicolumn Alignment

You can align Effectiveness... by

\multirow{2}{\dimexpr0.25\textwidth-2\arrayrulewidth-2\tabcolsep\relax}[-0.5cm]{...

Note [-0.5cm] and adjust it for vertical positioning. I have adjusted the column width such that they fit well within the text width.

\documentclass[11pt,draft]{article}
\usepackage{multirow}
\usepackage[table]{xcolor}
\usepackage{array}
\newcolumntype{C}[1]{>{\centering\arraybackslash}p{#1}}

\begin{document}
\begin{center}
\begin{table}[!htbp]
\noindent
\begin{tabular}{|c|C{\dimexpr0.25\textwidth-\arrayrulewidth-2\tabcolsep\relax}
           |C{\dimexpr0.25\textwidth-\arrayrulewidth-2\tabcolsep\relax}
           |C{\dimexpr0.25\textwidth-\arrayrulewidth-2\tabcolsep\relax}|}
\hline
\multirow{2}{\dimexpr0.25\textwidth-2\arrayrulewidth-2\tabcolsep\relax}[-0.5cm]{\centering \cellcolor{gray!50} Effectiveness of Controls} &    \multicolumn{3}{p{\dimexpr 0.75\textwidth-\arrayrulewidth-2\tabcolsep\relax}|}{\cellcolor{gray!50}\centering Probability of Threat Occurrence (Natural or Environmental Threats) or Threat Motivation and Capability (Human Threats)} \\
\cline{2-4}
\cellcolor{gray!50}
& \cellcolor{gray!50} Low & \cellcolor{gray!50} Moderate & \cellcolor{gray!50} High \\
\hline
%\rowcolor{white!50}
\cellcolor{gray!50} Low & Moderate & High & High \\
\hline
\rowcolor{white!50}
\cellcolor{gray!50} Moderate & Low & Moderate & High \\
\hline
\rowcolor{white!50}
\cellcolor{gray!50} High & Low & Low & Moderate \\
\hline
\end{tabular}
\caption{Risk Classifications}
\label{tab:xyz}

\end{table}
\end{center}
\end{document}