Ok, per that reasoning, tell hitters not to take pitches just so the runner can steal. Problem solved.
The main issue with this calculation is it doesn't take into account the first pitch of a count because it's impossible to steal a base before the batter sees the first pitch. Therefore times when the runner attempts to steal on the first pitch and the batter hits the ball are not included (or any time the runner is going and the batter hits the ball). You also have to take into account hit and run attempts, which certainly negatively affects the batter. If the batter doesn't hit the ball not only is he put in a worse count than he should have been (most likely because he attempted to hit a ball out of the strike zone) but it shows up as a stolen base attempt. They only way to truly find the stats is to determine the success of a batter when the runner has the green light, and it's not a hit and run. Stats cannot take that into account, and therefore the statistics are flawed.
The analysis is just way too simplistic and one of the things I hate when I see blind statistics used. So much of that is analysis in a vacuum and I can't go into all of it. Plus, the numbers have not just changed a bit. They have actually dramatically changed since 2004. I forget the exact number now, but stealing base success rate benefit is now something like 66% (I think there is a fangraphs article on this). Way different than the 75% claimed in the article.
BTW...when looking at ERT you have to take into account deltas because with zero men on you can still score, and then there is the expectancy of scoring at all vs. not scoring any runs which are different numbers. That would of course lead to the debate of the importance of scoring more runs but always scoring in bunches vs. scoring a little less but more consistently. Yet I will stay away from that.
edit: I will note the same thing I stated before. It will all come down to Hamilton getting on base. If he can get on a base at a good rate, he should be at the top of the order. If it's poor, he shouldn't. Basestealing should not be the main reason he is put at any spot in the order, be it first to "create havoc" or 7th so he is not stealing in front of Votto.