You can make an argument that essentially replacing a moderately priced piece of software (Aperture) with a free piece of software (Photos) isn't good for the bottom line, especially if Photos really is designed with some measure of professional tools in mind.
Yes, but that argument fits better with a company who derives significant income from s/w. That's not Apple though. Its primary money maker is hardware and offering free s/w is a way to hook in customers that want a "ready to use, all s/w included" computer. Plus with Photos being intricately linked to iCloud it does provide Apple with an additional monthly revenue stream, something that neither Aperture nor iPhoto provided while also encouraging users to buy into the entire Apple ecosystem. That's a better scenario for Apple than getting $79 one time from a tiny % of its user base.