Unfortunately it's not that simply gone
WPF scales strokes too when you apply a scale transform, and I can't see any built-in options to stop scaling. If you just load a Xaml DrawingImage into ShapeNode, you will get attached result:
<diag:ShapeNode x:Name="n1" Bounds="30,30,20,20" ImageAlign="Stretch">
<diag:ShapeNode.Image>
<!-- from DrawingImage example in MSDN -->
<DrawingImage>
<DrawingImage.Drawing>
<GeometryDrawing>
<GeometryDrawing.Geometry>
<GeometryGroup>
<EllipseGeometry Center="50,50" RadiusX="45" RadiusY="20" />
<EllipseGeometry Center="50,50" RadiusX="20" RadiusY="45" />
</GeometryGroup>
</GeometryDrawing.Geometry>
<GeometryDrawing.Brush>
<LinearGradientBrush>
<GradientStop Offset="0.0" Color="Blue" />
<GradientStop Offset="1.0" Color="#CCCCFF" />
</LinearGradientBrush>
</GeometryDrawing.Brush>
<GeometryDrawing.Pen>
<Pen Thickness="10" Brush="Black" />
</GeometryDrawing.Pen>
</GeometryDrawing>
</DrawingImage.Drawing>
</DrawingImage>
</diag:ShapeNode.Image>
</diag:ShapeNode>
The WPF diagram doesn't parse Xaml itself but just calls the WPF's DrawImage(ImageSource, Rect) method and apparently it works by applying a ScaleTransform internally. So if you convert your SVG images to Xaml drawings you'll still get same results.
You should be able to work around it if you load only Geometry objects from Xaml instead of full DrawingImage, and custom-draw the geometries from a derived node class or Draw event by setting the Geometry.Transform property to a scale that would fill the node instead of scaling the whole image. Geometry.Transform is local to the Geometry object and only affects its coordinates, so the stroke you use to draw it will not be scaled.
Alternatively you might try converting your SVG drawings to Xaml data templates that bind to the node size and apply these templates to WpfDiagram's TemplatedNode. I.e. the geometry elements would specify coordinates through {Binding} expressions that bind to node's width or height instead of relying on scale transforms.
I hope that helps,
Stoyan