I like to work at a much higher resolution than my intended final product in Wilbur because of the issues that you mention (among others). The nearly-parallel joins are my biggest issue with Wilbur's river flow output and I find that doing a blur on the terrain followed by a little noise and basin fill greatly reduces these effects. How much blur and how much noise depends on the parameters of your map, especially resolution. You want enough blur to deflatten the valleys, but not so much as to destroy the mountains.

If the developer of Wilbur will get off his lazy behind and use a rendering library that allows for alpha blending and antialiasing, then many of these issues that you show in your output would be greatly reduced. For now, working at a higher resolution and downsampling the image to a final size will act to smooth out the jagged edges somewhat (at the cost of making the rivers thinner overall). Throwing in a maximum operation before blurring will widen the rivers, but also mess up the joins just a bit.

It would also be nice if the developer would create a proper width algorithm for the rivers instead of requiring people to draw rivers in colors ranging from dark gray to white, blurring the output river mask in something like Photoshop, and then thresholding the resulting image to get an approximation of river width. It's tedious and the output isn't as good as a real river width algorithm would be.