R2D3 overwrites the console within the shadow DOM that contains the visualization code. This is why the console behavior is altered - which might look nice, but doesn't allow closer inspection of objects, or hiding of the console.
There don't appear to be any parameters that can modify this when creating the visualization. This leaves two options, modify the package or add a line of javascript to the visualization. I'll go with the latter here.
The document window itself still retains default console behavior, so we can use it to redefine the shadow DOM console behavior. In the visualization, at the top line add:
console = d3.window(svg.node()).console;
There are other methods of accessing the window, but this should be sufficient, and might be the shortest, it won't work for d3v3, which could use:
console = svg.node().ownerDocument.defaultView.console;
Yes, it is not ideal and a bit hacky, but it is certainly easier than changing the R source (and continuing to do so when the package is updated).