Interesting article, however there's a lot of speculation on what the conversations are in the board room and not necessarily facts.
It would make sense that Disney is more concerned with how much guests spend per day as opposed to increased guest traffic. Bottom line is that WDW, or any other resort, is bound by four walls, and you can only fit so many inside. The next logical step is to work on having those guests within the four walls to spend more. That or build another park, and I don't think that's likely for the foreseeable future.
I personally think that the reasoning behind 'locking in' guests to reservations doesn't hold water. As long as making fastpass reservations doesn't cost money, or your not financially penalized for missing your fastpass reservation, then some guests may not have a second thought on reserving a place in line at Disney and not using it. In fact, they may do that as a failsafe of sorts while their plan is to include a visit to another place like Universal. If for some reason they can't make it to Universal on a given day, then not to worry - I've got faspasses stashed away for the Magic Kingdom (maybe I'm missing something here, but I haven't found anything that tells me that making a fastpass reservation somehow financially obligates me to visiting the park that day). Granted this does imply that you've already purchased tickets to WDW, so you've already made a financial investment, but there's nothing to stop one from spreading out, say, a three day ticket across a week while they hop back and forth between the two complexes. I'm seeing more and more people planning a trip to 'central Florida' instead of 'Disney' to take advantage of all the attractions.
Being an IT person, I'll throw out there that the core of the discussion around fast passes and MyMagic+ isn't the only thing Disney has invested in. Yes they've spent close to two billion, but I suspect that a large portion of the investment is associated with other infrastructure upgrades and/or application development. Data mining and crowd management at the level Disney is thinking about takes a technology infrastructure that doesn't come cheap. I've seen complex installations get delayed and plagued by problems, but eventually they work themselves out. I see something similar happening here.
Bottom line is that I'm defending the practice, but I don't think that the expenditure is being done solely to pillage every guest. Disney knows full and well that they have to keep people coming back if they want the cash to flow. They'll keep doing the things that the guests want to see, just not at the rate that a lot of us would like.