The trains I've been on, two small children in the aisle would have kept any adult from getting down the aisle, unless the adult pushed/bumped them to the side. So in my mind, it's not the buggy that's the issue, it's the kids in the aisle when people are trying to get onto the train and into their seats.
If the buggy was small enough to get down the aisle, it was not causing the bottleneck. The children who were in the aisle were causing the bottleneck. Therefore it was not rude to ask them to clear the aisle.
In fact, if that photo is accurate, there is NO way any grownup could get past even one little boy.
Make it a grownup carrying a stroller and a child, plus one tote bag, and the problem is the same.
In fact, I would say that a slim stroller is probably the most sensible way to corral the stuff. The kid and the stroller become a single low, easy-to-maneuver, smoothly moving p=object. Until someone stands in the aisle.
(also, NYCs subways have people standing in the aisles, so they're not very wide.)
I guess she contributed to the problem by getting on the train in the first place. But personally, I'll excuse her for living.