You're right, writing it as a story does raise another set of issues. Most of the transitions here seemed reasonable, although a couple were definitely on the speculative side, along the lines of "I can imagine him thinking..." etc.
One important point is that just because something lacks quotation marks doesn't mean Bruce made it up. Vinge could've said it; it can just mean that as spoken, it was hard to understand or hard to read.
The value of writing it this way is providing a cohesive story with context and interpretation by the writer, who is familiar with the audience. Conversations bounce around, even as interviews the answers ramble all over the place. Reorganizing it afterwards into topics makes a lot more sense.
I could go on and on about the value of the format, but just writing it as a story doesn't make it a perfect one.