IMO Rufus' dead was pretty obvious(come on, he practically was shoted in the 'face' by a WEAPON), and it was intented to be that way.
Afterall, the end of the 2nd Disc is about ShinRa's fall, and the game presented it with the deads of the most important members of the Company, one by one. First it was Rufus, killed by a WEAPON. Second and third were Scarlet and Heidegher, killed inside the Proud Cloth. And fourth was Hojo, killed by the party after his mutation.
By presenting the story like that, I had the impression the game wanted to show us that ShinRa was really gone now, and only the planet's biggest threat(Sephiroth) remained.
I don't see why Squaresoft would make Rufus' dead look ambiguous on purpose.
But that's just me.