Yes and no. For remote embedding in most places, you cannot use JavaScript. One of my least favorite things about Flowplayer is the constant focus on using jQuery to load, embed, and control the player throughout the documentation. Do not want.
But with some work it is definitely possible to generate embed codes without JavaScript, and with the external configurations you can generate much smaller ones.
Here's the code I use on my site:
<embed src="http//[yourhost]/flowplayer.swf" flashvars="config=[url]" allowfullscreen="true" allowscriptaccess="always" quality="high" bgcolor="#000000" type="application/x-shockwave-flash" pluginspage="http//www.adobe.com/go/getflashplayer" width="480" height="294" wmode="opaque"></embed>
I removed the : from the URLs in the embed code, because the auto-linking on this site completely breaks them.
The way this works is that it loads a copy of Flowplayer which uses an external configuration file that is unique for each video (it's dynamically generated from a database on our site). That configuration file has everything that the player needs to play the video, including the plugin configuration and the playlist info. The only configuration other than that in the embed code is the width and height of the player, which need to be in the object tag.
Since it's just a basic object tag at this point it should be able to be embedded anywhere that supports them. You will need to generate and provide the embed code to your users on your own though, as Flowplayer will not generate it for you.