Hi,
That is the strength of other world languages like English too. So we need not feel ashamed to borrow words from other languages. People have already started using the word 'software' and it has got into many documents and books including textbooks. In the situation, my opinion is that we can stick with the word.
A good malayalam translation for "software", if it can convey the exact meaning, should always be welcomed. But IMHO "Ganana Soothram" and "Mruthu saamagri"(soft-ware!) fails to convey the exact meaning. If we couldn't find any suitable translation, we can adopt the word "software" itself, which will make our language "richer"