If it came down to having the same basic story of Star Trek XI
with or without Leonard Nimoy, I know which one I would choose. That is a major reason why the universe-hopping aspect of the movie was a good choice. It also makes it clear that the original, slightly inconsistent universe of TOS-ENT is still out there, just missing Romulus and Remus.
Besides the obvious authorial intent that Nimoy was playing the original Spock character, there is nothing he says to Kirk on Delta Vega that cannot be explained away. In fact, I'm sure Timo
has done this already someplace. My simple explanation is that Spock wanted Kirk to use his leadership abilities as early as possible, and anything he told Kirk was simply a means to that end. Of course, I tend to get less hung up on the inconsistencies as time goes by and simply accept that the creators are human. Whether they just messed up or want to tell a story that requires something besides slavish devotion to 40 years of continuity is beside the point.