According to the documentation, that's not allowed:
If you want to use an expression as a static value on your page or control, you use an expression as part of an ASP.NET server control. A typical strategy is to add a Literal control and set its Text property to an expression. For example, to place a copyright notice at the bottom of every page you could use the following:
<p align="center">
<asp:Literal runat="server" text="<%$ AppSettings: copyright %>"/>
</p>
This might help you if want to do it all in the aspx file:
<script type='text/javascript' src='<asp:Literal id="literal1" runat="server" text="<%$ AppSettings: jsSource %>" />'></script>
Note the unpleasant single quotes in the text variable - trying to us escaped double quotes results in "Badly formed script tag" errors.
Edit: apologies - I've swapped the order around this does work.