Perhaps concerned scientists and editors should reject the bifurcation here and take on the lingo of the field that creates the tool they have to use and need to learn better as a first step in learning to program in a more responsible manner?
http://scholar.google.com/scholar?hl=en&q=%22linear+alge...
"Code" also has connotations (self-contained, numerical, etc.) that make it distinct from "program" or even "library". A routine in ATLAS is a code, but Microsoft Word is not.
As one of many examples, here's a 1955 survey article compiling a list of "available digital computer codes for nuclear reactor problems": http://www.osti.gov/energycitations/product.biblio.jsp?osti_...
The bifurcation is still harmful to them even if the software usage originated later than the science term.