Okay! I found my own way to get baml files to convert xaml files:

1. Add System.Activities.Presentation reference to the ILSpy.BamlDecompiler project references.
2. In the KnownInfo.cs make the following changes:
   a. In the void LoadKnownAssemblies40() method:
   KnownAssemblyTable = new string[5]; -> KnownAssemblyTable = new string[6];
   KnownAssemblyTable[5] = "System.Activities.Presentation, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35";
   b. In the public KnownInfo(ITypeResolver resolver) method:
   KnownTypeTable = new TypeDeclaration[760]; -> KnownTypeTable = new TypeDeclaration[762];
   KnownTypeTable[0x2f8] = new TypeDeclaration(resolver, "ActivityDesigner", "System.Activities.Presentation", 5);
   KnownTypeTable[0x2f9] = new TypeDeclaration(resolver, "WorkflowViewElement", "System.Activities.Presentation", 5);

This should be enough though; however, it will still not going to work for xaml files containing "Grid"; because it gives the following error:
System.Xml.XmlException: 'Name' is a duplicate attribute name.
at System.Xml.XmlWellFormedWriter.AddAttribute(String prefix, String localName, String namespaceName)
at System.Xml.XmlWellFormedWriter.WriteStartAttribute(String prefix, String localName, String namespaceName)
at System.Xml.Linq.ElementWriter.WriteStartElement(XElement e)
at System.Xml.Linq.ElementWriter.WriteElement(XElement e)
at System.Xml.Linq.XElement.WriteTo(XmlWriter writer)
at System.Xml.Linq.XContainer.WriteContentTo(XmlWriter writer)
at System.Xml.Linq.XNode.GetXmlString(SaveOptions o)
at System.Xml.Linq.XNode.ToString()
at ILSpy.BamlDecompiler.BamlResourceEntryNode.LoadBaml(AvalonEditTextOutput output) in G:\BTAKADEMI\PortableApplications\IL Spy Source Code\ILSpy.BamlDecompiler\BamlResourceEntryNode.cs:line 68
at ILSpy.BamlDecompiler.BamlResourceEntryNode.<>c__DisplayClass3.b__1() in G:\BTAKADEMI\PortableApplications\IL Spy Source Code\ILSpy.BamlDecompiler\BamlResourceEntryNode.cs:line 36

If you get this error then you should also do the following;

1. In the BamlResourceEntryNode.cs file change the "bool LoadBaml(AvalonEditTextOutput output)" method as below:
   bool LoadBaml(AvalonEditTextOutput output)
   {
   var asm = this.Ancestors().OfType().FirstOrDefault().LoadedAssembly;
   Data.Position = 0;
   XDocument xamlDocument = LoadIntoDocument(asm.GetAssemblyResolver(), asm.AssemblyDefinition, Data);
   if (asm.AssemblyDefinition.FullName == "System.Activities.Core.Presentation, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35")
   {
   XmlReader reader = xamlDocument.CreateReader();
   reader.Settings.ValidationType = ValidationType.None;
   //You may change the file name "aaa.xaml" as you like...
   XmlTextWriter writer = new XmlTextWriter("aaa.xaml", System.Text.Encoding.UTF8);
   writer.Formatting = Formatting.Indented;
   while (reader.Read())
   {
   writer.WriteNode(reader, true);
   }
   writer.Flush();
   writer.Close();
   reader.Close();
   }
   output.Write(xamlDocument.ToString());
   return true;
   }

Finally this is definately working B~).