No ScriptLoader only adds scripts I have coded it to add and handles dependency logic for the included jquery and YUI features and various other features built into mojoPortal. It is not designed to add arbitrary scripts.
The ASP.NET ScriptManager can add scripts but it is no different in that you have to declare them in layout.master, and adding them with ScriptManager does not put them in the head, so if it really needs to go there you should put it there manually.
<asp:ScriptManager ID="ScriptManager1" EnablePageMethods="true" runat="server">
<asp:ScriptReference Path="~/pathtopyourscript.js" />