These motivations are understandable and they are regrettable. In any event a scientific paper should detail all of the analysis in sufficient detail that it can be reproduced. I wouldn't say source code would be required but certainly sufficient detail to re-implement any tools would be required. For sufficient analysis complexity maybe the source code would be the best documentation. One worry I have is the same as for electronic elections, what does it really mean if you just rerun the same tools and it spits out a number, any errors in the analysis will be faithfully reproduced which I think would impede scientific understanding.