The way I get around this limitation, is to turn my scripts into functions that take no arguments (if I need variables from the global namespace, I either explicitly pass them in the function, or use "evalin" to grab them.)
Then you can define all the additional functions you need in the "script." It's a hack, but I have found it to be quite powerful in those cases where I need several non-trivial functions.
EDIT: Here's a simplistic example. All this can reside in a single file.
function [] = myScriptAsAFunction()
img = randn(200);
img = smooth(img);
figure(1);
imagesc(img);
axis image;
colorbar;
end
function simg = smooth(img)
simg = img / 5;
end