IT DOESN'T MAKE ANY DIFFERENCE!
You have three active runners, none of which are out and you must have an individual base for each one!
Damn, come on, guys! Y'all overthinking this by a mile and a half.
If the obstructed runner was tagged OUT, the ball is dead. If the obstructed runner was not tagged out, the ball is live and R2 would be retired for the 3rd out.
However, if the BU told the obstructed runner to stay on the base, I would consider the ball dead as the umpire has now started assigning bases to the obstructed runner. That means that R2 cannot be ruled out under any circumstance. Was it screwed up by the BU, only if R1 was on the base when tagged with the ball.
Even if the umpire kicked the play on a misinterpretation of the rule, he cannot turn around and rule R2 out as the original call placed the runner in jeopardy.
See? Piece of cake