I picked the following trick from Gerd Stolpmann's findlib;

   exception Toplevel_error of string;;

   let toplevel_exec s =
     let l = Lexing.from_string s in
     let ph = !Toploop.parse_toplevel_phrase l in
     let fmt = Format.make_formatter (fun _ _ _ -> ()) (fun _ -> ()) in
       if not (Toploop.execute_phrase false fmt ph)
       then raise (Toplevel_error s)
   ;;


You can now do

   toplevel_exec "#load " ^ (String.escaped user_module) ^ ";;"

Regards -- Markus