The possibility is that Qui-Gon would be able to fulfill the father-mentor role for Anakin, which with Qui-Gon's death, was filled in by Palpatine. Obi-wan, while possibly being the best teacher for Anakin and a mentor...was not able to fill in as a father like role model. Only as a brother. This was where the loss of Qui-Gon hurts Anakin's chances (since it gives Palpatine an easy route into Anakin's life and trust).
However, we (the audience) should not underestimate Darth Sidious (nor the writers). Plans within plans, and new plans out of old plans. Qui-Gon would not be an insurmountable threat for Palpatine. It would just mean taking a different route to achieve the Sith's goals. Count Dooku might not even leave the order with Qui-Gon living, meaning Palpatine would need another to help him set in motion the clone army....or even come up either a different plan entirely. Darth Maul, depending on if he lives or not (completely I mean) seems to think that a criminal empire would be what is needed to draw out the Jedi, and they might have been the plan before Obi-wan happened....and Anakin was discovered. So Palpatine would need a different plan....or at the very least, a different stooge apprentice to poke Sifo-Dyas into making a clone army. Without Dooku, they might even get a different template...so no Jango Clones....no Boba Fett.
But Palpatine would come up with something regardless of the outcome on Naboo.