New setting "logPlayerCommands" (default true) which can be disabled to prevent player commands from being logged.

src/com/massivecraft/factions/Conf.java

@@ -100,6 +100,7 @@ public class Conf
 	public static boolean logLandClaims = true;
 	public static boolean logLandUnclaims = true;
 	public static boolean logMoneyTransactions = true;
+	public static boolean logPlayerCommands = true;
 	
 	public static boolean homesEnabled = true;
 	public static boolean homesMustBeInClaimedTerritory = true;

src/com/massivecraft/factions/P.java

@@ -172,6 +172,12 @@ public class P extends MPlugin
 		Conf.save();
 	}
 
+	@Override
+	public boolean logPlayerCommands()
+	{
+		return Conf.logPlayerCommands;
+	}
+
 	@Override
 	public boolean handleCommand(CommandSender sender, String commandString, boolean testOnly)
 	{

src/com/massivecraft/factions/zcore/MPlugin.java

@@ -167,6 +167,12 @@ public abstract class MPlugin extends JavaPlugin
 	// COMMAND HANDLING
 	// -------------------------------------------- //
 
+	// can be overridden by P method, to provide option
+	public boolean logPlayerCommands()
+	{
+		return true;
+	}
+
 	public boolean handleCommand(CommandSender sender, String commandString, boolean testOnly)
 	{
 		boolean noSlash = true;

src/com/massivecraft/factions/zcore/MPluginSecretPlayerListener.java

@@ -28,7 +28,8 @@ public class MPluginSecretPlayerListener implements Listener
 
 		if (p.handleCommand(event.getPlayer(), event.getMessage()))
 		{
-			Bukkit.getLogger().info("[PLAYER_COMMAND] "+event.getPlayer().getName()+": "+event.getMessage());
+			if (p.logPlayerCommands())
+				Bukkit.getLogger().info("[PLAYER_COMMAND] "+event.getPlayer().getName()+": "+event.getMessage());
 			event.setCancelled(true);
 		}
 	}
@@ -40,7 +41,8 @@ public class MPluginSecretPlayerListener implements Listener
 		
 		if (p.handleCommand(event.getPlayer(), event.getMessage()))
 		{
-			Bukkit.getLogger().info("[PLAYER_COMMAND] "+event.getPlayer().getName()+": "+event.getMessage());
+			if (p.logPlayerCommands())
+				Bukkit.getLogger().info("[PLAYER_COMMAND] "+event.getPlayer().getName()+": "+event.getMessage());
 			event.setCancelled(true);
 		}
 	}