Shinra fell apart during FFVII. All the top executives and most of the important faculty were killed in the WEAPON's assault on Midgar which destroyed most of the Shinra Tower, Meteor and Holy finished off the rest of it along with all of Midgar.

Junon was under Shinra control, yes, but there weren't many officials working there. The important people were in Midgar. The company surely collapsed without any figure of control. Though it seems Rufus did survive, Scarlet, Heidegger, Palmer and many of the other department heads, excluding Reeves, did get killed. Rufus didn't bother to show up until two years afterwards anyways.

I'd say it's safe to assume that Shinra is gone.

Rufus may be after power, but he's got little behind him except the Turks and the three clones. I'd say he's after something else.