It all depends on how you develop the Sith idea.

When I was working on my NPT, the Sith were a proactive offshoot of the Jedi, who wore dark cloaks and masks to hide their identities from their brothers.

If you want the whole "force religion" to be concidered ancient by the OT, you can use the NPT to discredit the Jedi. Remember: the Jedi ONLY use the force for knowledge and defense. During the Clone Wars they would help with strategy, but I don't think they would lead assaults. This could lead to the general populace feeling the Jedi might be disloyal. They shouldn't be creeps like in the PT, but the other characters and the audience may see their traditions, beliefs and actions as ineffectual considering the darker times.

In my NPT EPI, Anakin inadvertantly inspires the creation of the Sith Order. This was revealed in my EPII, which was a mystery of who these dark clad warriors were. By EPIII, Palpatine is made Emperor and tells the Jedi that their assistance, lacking as it is, is no longer required. The Sith are greeted in the Senate chamber with cheers because they are willing to do what is necessary to end the Clone Wars.

My goal was to have the audience agree with the people of the republic and the sith up to EPIII where they would feel... oops, this has gone too far.