I believe one of the options you can take is to save the figure to disk without rendering the figure window. Please refer to the code below and see if it would be a good option for you.
h = figure('Visible','Off'); % Creating a figure and not displaying it
ax = axes; % Create an Axes;
plt = plot(ax,1:10,1:10,'r'); % Plot an arbitrary line in the axes
set(h,'CurrentAxes',ax); % Set current Axes of figure to 'ax'
print(h,'-djpeg','fname.jpeg')% Print the plot to file 'fname.jpeg'
% exportgraphics(h, 'myfilename.png'); % An alternative for "print".
