We can remove this information through modifying linux-3.2/arch/arm/mach-omap2/omap_hwmod.c

--- linux/arch/arm/mach-omap2/omap_hwmod.c.orig    2012-06-12 16:13:11.166367276 +0200
+++ linux/arch/arm/mach-omap2/omap_hwmod.c    2012-06-12 16:15:56.319482962 +0200
@@ -781,6 +781,8 @@
                          oh->prcm.omap4.clkctrl_offs);
 }
  
+#define WD_FILTER    "wd_timer2"
+
 /**
  * _omap4_disable_module - enable CLKCTRL modulemode on OMAP4
  * @oh: struct omap_hwmod *
@@ -807,10 +809,10 @@
             oh->prcm.omap4.clkctrl_offs);
  
     v = _omap4_wait_target_disable(oh);
-    if (v)
-        pr_warn("omap_hwmod: %s: _wait_target_disable failed\n",
-                oh->name);
-
+    if (v) {
+        if (strcmp(oh->name, WD_FILTER))
+            pr_warn("omap_hwmod: %s: _wait_target_disable failed\n", oh->name);
+    }
     return 0;
 }