micdsguy,
I'm not an expert on baseball rules history (or current baseball rules for that matter) so I don't know for sure if the "abandoned effort rule" existed in 1908.
Let's assume (yeah, I know) that it did.
If the ump called Merkle out (3rd out) for abandoned effort before the runner from third touched the plate the run would not have counted. If he called him out after the runner touched the plate then the run would count.
Now lets look at the facts from the perspective of the base umpire:
a) The game/pennant is on the line.
b) The winning run for the Home Team (Giants) is about to be scored.
c) If I call this runner out too soon the run will not score.
d) I am working in front of thousands of Giants fans.
e) I think I'll watch the runner touch the plate before I decide.
Yes, that was all tongue-in-cheek. If that did happen, the defense would have appealed that Merkle didn't touch second base. (an apparent 4th out) That appeal would have been upheld and the run would have been negated anyway.