It's perfectly possible using Flash's externalInterface and the JavaScript you're writing yourself alone (which should be the only JavaScript you'll need).
SWFObject exists only to abstract away adding Flash pieces to HTML content, so it's not necessary at all (it's basically going to write the proper object
and embed
tags depending on your browser and work around the IEs' ActiveX
click-to-run-Flash warnings).
If you wanted to hand-code your Flash piece into a document, that's perfectly fine; SWFObject makes it cleaner and easier but doesn't enable or add functionality beyond that. However, because it works so well, it's become kind of a standard method to get Flash on a site.
Drop your Flash piece on a page however you'd like, make sure it has an id
set in its object
and embed
tags and you should be set.