....CVS saw that there were more benefits to be made handling prescription drugs than selling diapers.
1. There is no "by" because it is not needed for the sentence to be grammatically correct. If there would be a by where you mentioned, there should also be a 'by' between 'than' and 'selling'.
2. No, you cannot replace it as such. It's a comparison. Keyword: than. The comparison is ' handling prescription drugs' and 'selling diapers'. If you would replace it with "to be made to handle" you are changing that was is compared, "handling" to > "to handle", which would mean the sentence wouldn't make sense anymore.