Count Qui-Gon wouldn't have a red sabre if he wasn't a Sith Lord, mute point anyways seeing as there is no way of replacing Christopher Lee with Liam Neeson.
The nearest I think we can get around this is by adding Dooku to TPM and having his formation of the Seperatist movement a reaction to the sort of narrow thinking that could get Qui-Gon killed and allow a Sith Lord to take over the government.