The short answer is that, yes, you just print to the browser. You must begin with a correct Content-type-header, then two linefeeds and then you print the SWF data to the browser.

Something like

print "Content-type: application/x-shockwave-flash\n\n";
print $SWFdata;

would suffice as a really simple SWF-on-the-fly-generation-CGI- script. You get the picture.

The part where you generate $SWFdata is obviously the non-trivial part, but you seem to have solved that already. If I remember correctly, there is a SWF-creation module that's perhaps worth checking out.