All markers in a series will have the same color, so the best approach I can think of is to plot two separate series, one with red markers and the other with blue.
t=0:0.1:2*pi;
figure
sine=sin(t);
cosine=cos(t);
plot(sine(1:2:end),cosine(1:2:end),'r.')
hold on
plot(sine(2:2:end),cosine(2:2:end),'b.')
hold off
xlim([-1.25 1.25])
ylim([-1 1])
axis equal
