I don't think "being at the same disadvantage" is as much of an equalizer in baseball as in other sports. Baseball isn't a head-to-head game, so each team will need to execute separately and we know how much baseball is subject to chance to begin with. Maybe citing no more 100-game winners is a bit much (since you could still win 100 games), but I'd argue making extra innings that much more precarious really removes more player skill than necessary. These are supposed to be world class ball players and now they're working with rules that are less designed to make things fair than they are to be marketable. I totally agree with fatcow when he says if the rule isn't good enough for "important games" then it probably doesn't bring much to the game anyway.
I think this proposal is much closer to a baseball shootout too. It's almost a gimme scoring opportunity. Equally pulling personnel off the ice doesn't make the game any less of a game of hockey, but removing a player from the baseball field means you're opening up an exploitable gap.
But I actually think it's worse than a shootout since in hockey you can't score goals in bunches. Home runs will be particularly devastating since it'll just be gifting an extra run to teams. It's a lot harder to recover from a two-run deficit than a one-run deficit. If a team hits a lead off homer in the top of the inning, it'll be awarded an extra run because of the guy on second that they didn't earn. Suddenly the home team has to do a lot more than small ball their way into a tie, and the disadvantage starts looking more lopsided. Or what if the away team small balls the run in for a one-run lead and the home team hits a lead off home run the next inning, winning the game because of the free runner the MLB placed for them?