I think you have the chronology backwards. The use of "code" as a mass noun dates to the 1960s at the earliest (actually, I can't find a good example before the 1970s in brief searching), while the use of "code" as a singular noun to mean "implemented algorithm", and "codes" as the plural, dates back at least to the 1950s.
My Chronology may still be backwards, but they still should swap over to the language of the mature field of software development's language to better allow themselves to integrate in good practices.
The bifurcation is still harmful to them even if the software usage originated later than the science term.
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_...