If the team had believed earnestly that Sephiroth was a Cetra, then there'd be no problems - they wouldn't bother pursuing him since their goals coincided. It wouldn't make a whole lot of sense to go through this pretence... look at it this way:

1: Party believes Sephiroth is a Cetra - they follow, to find out his evil plans and so Aeris can learn about herself.

2: Party believes that Sephiroth's power comes from an evil, infectious alien that wants to destroy everything - they follow, to find out his evil plans and stop them.

Same result either way.