I don't really know all that much about Stallman himself, but doctorates (and degrees in general) are awarded a bit arbitrary anyway. I don't see what's less valuable about an honorary degree. I'd be more inclined to look at which universities it is that award the doctorates, honorary or not. Here, Stallman has an honorary degree from KTH in Sweden. There aren't all that many tech universities with a higher pedigree than KTH.