CodeShop ngx_http_smooth_streaming module patch, whichs adds configuration flag ism_rewrite_engine {on=default|off}; You can disable built-in rewrite engine with this patch. Applies to version 1.4.24; sample configuration: http://pastebin.com/HY9Wy6TD

ngx_http_smooth_streaming-1.4.24-ism_rewrite_engine.patch

diff -ur orig.nginx_mod_smooth_streaming-1.4.24/src/ngx_http_streaming_module.c nginx_mod_smooth_streaming-1.4.24/src/ngx_http_streaming_module.c
--- orig.nginx_mod_smooth_streaming-1.4.24/src/ngx_http_streaming_module.c	2011-04-24 16:55:51.000000000 +0200
+++ nginx_mod_smooth_streaming-1.4.24/src/ngx_http_streaming_module.c	2011-12-21 01:21:03.058062179 +0100
@@ -70,6 +70,13 @@
 */
 #endif
 
+/**
+ * Configuration structure for the smooth streaming module.
+ */
+typedef struct {
+    ngx_flag_t rewrite_enable;       /* built-in rewrite engine is enabled */
+} ngx_http_smooth_streaming_srv_conf_t;
+
 static char* ngx_streaming(ngx_conf_t* cf, ngx_command_t* cmd, void* conf);
 #if defined(BUILDING_SMOOTH_STREAMING)
 static ngx_int_t ngx_http_streaming_init(ngx_conf_t* cf);
@@ -77,6 +84,11 @@
 
 static ngx_int_t ngx_streaming_handler(ngx_http_request_t *r);
 
+static void *
+ngx_http_smooth_streaming_create_srv_conf (ngx_conf_t *cf);
+static char *
+ngx_http_smooth_streaming_merge_srv_conf (ngx_conf_t *cf, void *parent, void *child);
+
 static ngx_command_t ngx_streaming_commands[] =
 {
   {
@@ -91,6 +103,18 @@
     0,
     NULL
   },
+  {
+#if defined(BUILDING_H264_STREAMING)
+    ngx_string("mp4_rewrite_engine"),
+#elif defined(BUILDING_SMOOTH_STREAMING)
+    ngx_string("ism_rewrite_engine"),
+#endif
+    NGX_HTTP_MAIN_CONF|NGX_HTTP_SRV_CONF|NGX_CONF_FLAG,
+    ngx_conf_set_flag_slot,
+    NGX_HTTP_SRV_CONF_OFFSET,
+    offsetof(ngx_http_smooth_streaming_srv_conf_t, rewrite_enable),
+    NULL
+  },
   ngx_null_command
 };
 
@@ -106,8 +130,8 @@
   NULL,                          /* create main configuration */
   NULL,                          /* init main configuration */
 
-  NULL,                          /* create server configuration */
-  NULL,                          /* merge server configuration */
+  ngx_http_smooth_streaming_create_srv_conf,                          /* create server configuration */
+  ngx_http_smooth_streaming_merge_srv_conf,                          /* merge server configuration */
 
   NULL,                           /* create location configuration */
   NULL                            /* merge location configuration */
@@ -134,6 +158,30 @@
   NGX_MODULE_V1_PADDING
 };
 
+static void *
+ngx_http_smooth_streaming_create_srv_conf (ngx_conf_t *cf)
+{
+    ngx_http_smooth_streaming_srv_conf_t  *conf;
+
+    conf = ngx_pcalloc(cf->pool, sizeof(ngx_http_smooth_streaming_srv_conf_t));
+    if (conf == NULL) {
+        return NGX_CONF_ERROR;
+    }
+    conf->rewrite_enable = NGX_CONF_UNSET;
+    return conf;
+}
+
+static char *
+ngx_http_smooth_streaming_merge_srv_conf (ngx_conf_t *cf, void *parent, void *child)
+{
+    ngx_http_smooth_streaming_srv_conf_t *prev = parent;
+    ngx_http_smooth_streaming_srv_conf_t *conf = child;
+
+    ngx_conf_merge_value(conf->rewrite_enable, prev->rewrite_enable, 1);
+
+    return NGX_CONF_OK;
+}
+
 static ngx_int_t open_path(ngx_http_request_t *r, ngx_http_core_loc_conf_t *clcf,
                            ngx_str_t *path, ngx_open_file_info_t *of)
 {
@@ -228,6 +276,22 @@
   char const* query_first = (char const*)r->args.data;
   char const* query_last = query_first + r->args.len;
 
+  // get configuration
+  ngx_http_smooth_streaming_srv_conf_t *srv_cfg;
+#ifdef BUILDING_H264_STREAMING
+  srv_cfg = ngx_http_get_module_srv_conf(r, ngx_http_h264_streaming_module);
+#endif
+#ifdef BUILDING_SMOOTH_STREAMING
+  srv_cfg = ngx_http_get_module_srv_conf(r, ngx_http_smooth_streaming_module);
+#endif
+
+  // don't do anything if rewrites are disabled
+  if (!srv_cfg->rewrite_enable) {
+    //ngx_log_debug2(NGX_LOG_DEBUG_HTTP, r->connection->log, 0,
+    //  "ngx_streaming_rewrite_handler: rewrite disabled by server configuration.");
+    return NGX_DECLINED;
+  }
+
   if((r->method & (NGX_HTTP_GET|NGX_HTTP_HEAD) &&
       mp4_rewrite_get(path_first, path_last, query_first, query_last,
                       new_path, sizeof(new_path), new_args, sizeof(new_args))) ||
@@ -260,6 +324,23 @@
   ngx_open_file_info_t of;
   ngx_http_core_loc_conf_t *clcf;
 
+  // get configuration
+  ngx_http_smooth_streaming_srv_conf_t *srv_cfg;
+#ifdef BUILDING_H264_STREAMING
+  srv_cfg = ngx_http_get_module_srv_conf(r, ngx_http_h264_streaming_module);
+#endif
+#ifdef BUILDING_SMOOTH_STREAMING
+  srv_cfg = ngx_http_get_module_srv_conf(r, ngx_http_smooth_streaming_module);
+#endif
+
+  // don't do anything if rewrites are disabled
+  if (!srv_cfg->rewrite_enable) {
+    //ngx_log_debug2(NGX_LOG_DEBUG_HTTP, r->connection->log, 0,
+    //  "ngx_streaming_post_rewrite_handler: rewrite disabled by server configuration.");
+    return NGX_DECLINED;
+  }
+
+
   last = ngx_http_map_uri_to_path(r, &path, &root, 0);
   if (last == NULL)
   {
@@ -430,10 +511,18 @@
   }
 
   mp4_split_options_t* options = mp4_split_options_init();
-  if(r->args.len && !mp4_split_options_set(options, (const char*)r->args.data, r->args.len))
-  {
-    mp4_split_options_exit(options);
-    return NGX_DECLINED;
+  if (r->args.len) {
+    if(!mp4_split_options_set(options, (const char*)r->args.data, r->args.len))
+    {
+      mp4_split_options_exit(options);
+      ngx_log_error(NGX_LOG_ERR, r->connection->log, 0, 
+        "Client sent smooth streaming request with unparseable query string.");
+      return NGX_DECLINED;
+    }
+  } else {
+    ngx_log_error(NGX_LOG_ERR, r->connection->log, 0, 
+      "Client sent smooth streaming request without query string.");
+    return NGX_HTTP_BAD_REQUEST;
   }
 
   log = r->connection->log;