Until Disc 3, Sephiroth had a barrier around the Crater which kept everything out. It's not until right before the fight with Diamond that it's taken out. So, after that, only Ultimate, Ruby, and Emmy are alive. All three of them are included, as Kishi said, for game mechanics: they all give valuable items. Diamond and Sapphire are the only ones that aren't, and both of them attacked Shinra's main bases. As I said before, more power to them. heh

The crisis that summoned the Weapons was not Sephiroth, nor Jenova. Both of them were on the Planet for years beforehand. It was Meteor. How, exactly, would you reccomend going to attack a meteor?
Also, I don't think the Weapons are intelligent enough to know a strategy, so they wouldn't have known about Holy and such.