Maybe not quite
that extreme, but yes, I want academia to reward good software at least as well as it rewards mediocre papers.
NumPy is unusual because it's so broadly useful: physicists and neuroscientists can use it (like original authors), but so can quants and ad analytics folks and other people with serious budgets. Enthought and Continuum exist because they can tap into those markets, and, as a result, Travis (&ct) ended up doing very well--and justifiably so. However, most scientific software is more specialised or lacks this industrial backstop, and I don't see how they could follow a similar path. There's no serious industrial application for spike sorting, for example, but it's very important to neuroscience research.
I'm not sure I understand your concern about throngs of dishonest people, or least how it is any different from the status quo.
I am not imagining a system where money and jobs are just thrown around. Instead, I just want minor changes in hiring and funding. Academic promotion/hiring already weighs a bunch of factors: publication record, funding, peer evaluations, teaching, and various forms of service. I think writing and maintaining a widely used software package is currently under-valued there. Maintaining very popular packages might be treated as editing a journal, another form of academic service that does seem to count for something.
Similarly, it is (comparatively) easy to get money to develop new methods and write some code implementing them. There ought to be a complementary funding stream for maintaining successful packages once they are written. You could imagine a BAA-like process where applicants say, "My toolbox was downloaded 2,182 times and cited in 378 papers last year. However we've got a bunch of open issues including integration with X, Y, and Z, missing documentation for A, B, and C, and so. I want...20% salary support to work on this over the next year and $10,000 for a freelance technical writer." As with other grants, these would be evaluated (potential impact, proposer's track record, interactions with other funded programs, etc).
I realize there are alternatives. Stephen Wolfram essentially took Symbolic Manipulation Program "private" and funded Mathematica development by selling subscriptions. It worked for him, though I think that's asking people to assume a huge career risk or change that they might not want.
I wonder the SageMath guy ever considered something like the NIH's SBIR program (a scheme for setting up small businesses based on research).