This isn't fixed in Unity 5.5.0 as I still get this in 5.5.2f1. Thanks to @as-andrew for his canvas.renderMode = RenderMode.ScreenSpaceOverlay solution as that got me experimenting to find my own solution. Setting just the renderMode did not work for me, I also had to set the worldCamera to null. Just setting the worldCamera to null didn't work alone. So the following allowed me to delete my canvas...

myCanvas.worldCamera = null;
myCanvas.renderMode = RenderMode.ScreenSpaceOverlay;
Destroy(myCanvas, 0.1f);

As the canvas I was deleting belongs to a child of a game object with a canvas of its own, performing the above will also change the same values for the parent canvas. So I had to fix the parent canvas values after the child canvas was deleted. So I added a behaviour that set my main canvas values every frame.

mainCanvas.renderMode = RenderMode.ScreenSpaceCamera;
mainCanvas.worldCamera = Camera.main;

Very hacky, but it works in my case.

I have the same problem. It is the camera with the render target. If I disable the camera in the scene or delete it from the scene, everything works well.
As long as the camera is enabled the Unity editor hangs spinning in an infinite loop when destroying a gameobject.

It's rather unbelievable that this fix is stuck in beta still. Can you please push this to a live version of Unity. I'm getting tired of this bug. I don't understand how anyone can even design a game with the engine right now with this bug active. The only work around I have found to work is to sequentially delete any child object in the canvas then delete the canvas if it's empty. A total pain in the butt and a very slow solutions.

We are also running into this problem in our project. Until the fix is in a stable release, a work-around that has worked for us was to set the Canvas.renderMode to anything not World Space (ie. canvas.renderMode = RenderMode.ScreenSpaceOverlay) before destroying or disabling it.

Ran into this today. Glad to see a fix coming.

Have the same problem since i added a second camera for making a minimap!

Quick note to Anyone having this problem, we started experiencing this around the same time we'd added a new camera into our scene. Disabling this extra camera allowed us to SetActive(false) and Destroy() world space canvases again.

Also, just a note to Unity guys who may fix this, the Camera we'd added has a target render texture set.

Just bumped into this... We're switching necessary canvases to screen space until a fix comes out - obviously it doesn't behave as we'd intended but I'm hoping a work-around will come out ASAP so we can switch them back safely.

We are seeing a crash of the Unity editor (5.4.0f3 and 5.4.0p2) when a particular game object is fed into GameObject.Destroy(). The stack back trace looks like this, could it be the same issue?

d3d11!CContext::TID3D11DeviceContext_Unmap_<1>+0x4
Unity!GeometryJobTasks::EndGeometryJobFrame+0x130
Unity!GfxDeviceWorker::RunCommand+0x131d
Unity!GfxDeviceWorker::Run+0x2f
Unity!GfxDeviceWorker::RunGfxDeviceWorker+0x4d
Unity!Thread::RunThreadWrapper+0x38
kernel32!BaseThreadInitThunk+0x14
ntdll!RtlUserThreadStart+0x21