To disable core units, you need to replace all the pioneer unittypes with a new one.
This is the list of the pioneers:
Unit_Pioneer_Altarian
Unit_Pioneer_Amarian
Unit_Pioneer_Ironeer
Unit_Pioneer_Krax
Unit_Pioneer_Mancer
Unit_Pioneer_Quendar
Unit_Pioneer_Tarth
Unit_Pioneer_Trog
Unit_Pioneer_Urxen
Unit_Pioneer_Wraith
Disable them by introducing a new Prerequisite that cannot be fulfilled within your game, and put it in all those copied unittypes. For example,
<Prereq>
<Type>Tech</Type>
<Attribute>Thisdoesnotexistnorwillitever</Attribute>
</Prereq>
ex, your altarian pioneer unittype would look like this
<UnitType InternalName="Unit_Pioneer_Altarian">
<DisplayName>Pioneer</DisplayName>
<Description>Pioneers are equipped with the necessary materials to start new settlements.</Description>
<Class>Pioneer</Class>
<RaceType>Race_Type_Altarians</RaceType>
<CanBeDesigned>1</CanBeDesigned>
<Gender>Female</Gender>
<AdditionalTrainingTurns>30</AdditionalTrainingTurns>
<IsSovereign>0</IsSovereign>
<IsStartingUnitType>1</IsStartingUnitType>
<GameModifier>
<ModType>Unit</ModType>
<Attribute>UnlockAction</Attribute>
<StrVal>BuildTown</StrVal>
</GameModifier>
<GameModifier>
<ModType>Unit</ModType>
<Attribute>UnlockAction</Attribute>
<StrVal>BuildImprovement</StrVal>
<StrVal2>Outpost</StrVal2>
</GameModifier>
<LevelMilestone InternalName="L1">
<Level>1</Level>
<UnitStat_CombatSpeed>20</UnitStat_CombatSpeed>
<UnitStat_Constitution>10</UnitStat_Constitution>
<UnitStat_Dexterity>9</UnitStat_Dexterity>
<UnitStat_Intelligence>9</UnitStat_Intelligence>
<UnitStat_Strength>8</UnitStat_Strength>
</LevelMilestone>
<SelectedAbilityBonusOption>Weak</SelectedAbilityBonusOption>
<Equipment>K_Female_Head_02</Equipment>
<Equipment>Sovereign_Bandit_Hair_ID1</Equipment>
<Equipment>Quilted_Corset_ID1</Equipment>
<Equipment>Empire_Overskirt_ID2_Flipped</Equipment>
<Equipment>TightBoots_Dark</Equipment>
<Equipment>SionVambraces</Equipment>
<Prereq>
<Type>Race</Type>
<Attribute>Race_Type_Altarians</Attribute>
</Prereq>
<Prereq>
<Type>Tech</Type>
<Attribute>Thisdoesnotexistnorwillitever</Attribute>
</Prereq>
<AnimationPack>FemaleSovereignAnimationPack</AnimationPack>
<BattleAnimationBehavior>Melee</BattleAnimationBehavior>
<BobbingFrequency>0</BobbingFrequency>
<ClothPoseIndex>6</ClothPoseIndex>
<Color_Hair>163,118,83,255</Color_Hair>
<Color_Metal>145,145,145,255</Color_Metal>
<Color_Skin>210,145,95,255</Color_Skin>
<CutSceneDataPack>DefaultUnitCutscenePack</CutSceneDataPack>
<EyeTexture>gfx\eyes\blinks\eyeblink_f2_ltblue.png</EyeTexture>
<InfoCardBackground>BG1_Sunset</InfoCardBackground>
<InfoCardBackgroundFlipped>0</InfoCardBackgroundFlipped>
<ModelPath>Gfx\HKB\Units\K_Female_Mesh_01.hkb</ModelPath>
<ModelScale>1</ModelScale>
<MovementType>land</MovementType>
<MovingSFX>TEMP_KnightMarching1</MovingSFX>
<OnHitParticleName>Bloody_OnHit</OnHitParticleName>
<SkeletonPath>Gfx\HKB\Units\K_Male_Skeleton_01.hkb</SkeletonPath>
<SoundPack>SoundPack_Generic_Female</SoundPack>
<TacticalModelScale>1.5</TacticalModelScale>
<Texture_Eyes>gfx\eyes\blinks\eyeblink_f2_ltblue.png</Texture_Eyes>
<Texture_Skin>K_Female_Freckles_Texture_01.png</Texture_Skin>
<UnitModelType>KingdomFemale</UnitModelType>
</UnitType>
After this, there is still one pioneer that you can gain from a quest. But we are not getting quests currently so I won't go into that.