I think the problem is fundamentally one of economics. Research is good, but you have to decide how much money to allocate to it. In order to decide, you need a metric for performance. Really, only scientists are qualified to judge whether the results of other scientists are worth anything, so currently the only metric we really have is publishing in peer-reviewed journals. Ultimately, therefore, that's where the incentives end up.
When a more appropriate way of quantifying research output and its benefits is found, hopefully a beneficial change in culture will trickle down into the academic trenches.
How about trying to fix the current system by making somebody else using your software count as a "super citation"? (It could even arguably count as much as co-authorship.)
I think this is an excellent idea. If published software could be tagged via a unique identifier (like the DOI of a paper), then it could be cited by that tag just like a paper. Well written software might even get cited more than the paper it was published in.
When a more appropriate way of quantifying research output and its benefits is found, hopefully a beneficial change in culture will trickle down into the academic trenches.