I will troll this person's ass.

The issue here is not whether Shin-Ra was bad or not, they are dicks who deserve what they got. The issue here, is that Shin-Ra, as the most powerful human force on the Planet is actually trying to use all their fancy technology and military power to stop Sephiroth and the party decides they need to be taken out, (and let's ignore the fact that Cloud and Co have been trying to ignore them up until this point, focusing more on Sephiroth until now) even though they are actually trying to save the planet for once (so they can go back to ruling it and sucking it dry of mako) but they are actually doing something whereas your party is basically twittling their little thumbs with nothing to do and decide Shin-Ra is just not up to any good, and they should stop them from trying to save the planet.

It's akin to if Kefka, instead of ruling the ruined world like a petty dictator, actually used his power to build a half decent world without the empire to deal with but your party decided he needs to be killed anyway. No one would deny that kefka wouldn't deserve it from his action in the world of balance but to have them actually do something good, even if they had more selfish motives, and then watch your party take them down for no good reason.

No one really stops to think that maybe Shin-Ra should be left to try their plan. Its not like the party had some true reason to save the Huge Materia, it would weaken the planet but it could have saved it too if it weren't for hindsight and the knowledge of a third disc. The issue here is that Cloud and Co. really had no reason to go after Shin-Ra at this point cause they were both fighting for the same result even if they had different motives, while I don't feel this means Cloud and Co. should be helping Shin-Ra, it just seems very counter intuitive for them to be hindering them at this point. If Meteor dropped, it doesn't matter if you saved the four Huge Materias, the Condors, or one trashy little city or two. Everyone would be dead, Cloud and Co. just lucked out to learn that Aerith set Holy in motion and thus their actions against Shin-Ra are seen as less stupid and more virtuous, but objectively speaking, they were foolish to try and stop Shin-Ra.