It seems to me that Jacob was pretty unresponsive to the fact that the lighthouse mirrors got smashed. He seems to know the candidates pretty well, seeing as he know Hurley would need to actually be told what to do, and Jack would need to "stare at the ocean for a while." I think he knew that Jack would react the way he did in the lighthouse and smash the mirrors. Whoever is coming to the island is going to get there regardless of the lighthouse.

So, if this is true, why would Jacob want to take out the lighthouse? Maybe Smocke can use it for his purposes and Jacob didn't want that to happen. Maybe Smocke needs it to get off the island?

very likely. also, he got the two last remaining candidates out of the temple, where they were supposedly protected.

Someone mentioned in another thread that maybe MiB was going to use the lighthouse to bring in reinforcements... this would be a likely way for Jacob to thwart that plan without directly interfering, which it seems like he can't do (especially being dead and all).