Increase the initial output of each neutral faction tier one building and allow them to compete with major factions but only as a one city wonder--disallowing them to create additional pioneers. If the buildings are based off either the kingdom's or empire's building mechanics, then increasing the bonuses substantially for when the city upgrades into the next level could be a likely work around.

Having their unique resource only be available through trade would also increase the reason to keep them around, provided the unit was available and unique enough to serve both factions.