XComGameData.ini modification:
Copy paste the following line instead of original.

+Loadouts=(LoadoutName="SquaddieRogue", Items[0]=(Item="SMG_CV"), Items[1]=(Item="Holotargeter_CV"))

XComClassData.ini modification:
Copy paste following lines to whole page.

;A configuration File

[XComGame.X2SoldierClass_DefaultClasses]
+SoldierClasses=TheRogueClass

[TheRogueClass X2SoldierClassTemplate]
+bMultiplayerOnly=0
+ClassPoints=4
;+IconImage="img:///UILibrary_StrategyImages.X2StrategyMap.MissionIcon_BlackMarket"
;+IconImage="img:///UILibrary_RogueMod.icon"
+IconImage="img:///UILibrary_RogueMod.class_rogue"
+NumInForcedDeck=1
+NumInDeck=4
+KillAssistsPerKill=3
+SquaddieLoadout=SquaddieRogue
+AllowedWeapons=(SlotType=eInvSlot_PrimaryWeapon, WeaponType="rifle")
+AllowedWeapons=(SlotType=eInvSlot_SecondaryWeapon, WeaponType="holotargeter")
+AllowedWeapons=(SlotType=eInvSlot_HeavyWeapon, WeaponType="heavy")
+AllowedArmors="soldier"
bAllowAWCAbilities=1
ExcludedAbilities="LightningReflexes"
ExcludedAbilities="Phantom"
ExcludedAbilities="Stealth"
ExcludedAbilities="EverVigilant"
ExcludedAbilities="CoveringFire"
ExcludedAbilities="Sentinel"
+SoldierRanks=( aAbilityTree=( (AbilityName="Holotarget", ApplyToWeaponSlot=eInvSlot_SecondaryWeapon), (AbilityName="HuntersInstinct2", ApplyToWeaponSlot=eInvSlot_Unknown)), aStatProgression=((StatType=eStat_Offense,StatAmount=3), (StatType=eStat_HP,StatAmount=1), (StatType=eStat_Strength,StatAmount=0), (StatType=eStat_Hacking,StatAmount=35), (StatType=eStat_CombatSims,StatAmount=1)), )
+SoldierRanks=( aAbilityTree=( (AbilityName="IsmsFragileGhost"), (AbilityName="LoneWolf", ApplyToWeaponSlot=eInvSlot_Unknown), (AbilityName="IsmsScoutPack") ), aStatProgression=((StatType=eStat_Offense,StatAmount=3), (StatType=eStat_HP,StatAmount=1), (StatType=eStat_Strength,StatAmount=0), (StatType=eStat_Hacking,StatAmount=5), (StatType=eStat_CombatSims,StatAmount=0)), )
+SoldierRanks=( aAbilityTree=( (AbilityName="RapidTargeting", ApplyToWeaponSlot=eInvSlot_SecondaryWeapon), (AbilityName="RogueAndGun", ApplyToWeaponSlot=eInvSlot_PrimaryWeapon), (AbilityName="IsmsScoutsOverwatch", ApplyToWeaponSlot=eInvSlot_PrimaryWeapon) ), aStatProgression=((StatType=eStat_Offense,StatAmount=3), (StatType=eStat_HP,StatAmount=1), (StatType=eStat_Strength,StatAmount=0), (StatType=eStat_Hacking,StatAmount=5), (StatType=eStat_CombatSims,StatAmount=0)), )
+SoldierRanks=( aAbilityTree=( (AbilityName="ConcussiveShot", ApplyToWeaponSlot=eInvSlot_Utility, UtilityCat="pistol"), (AbilityName="ReturnFire3", ApplyToWeaponSlot=eInvSlot_Utility, UtilityCat="pistol"), (AbilityName="HDHolo", ApplyToWeaponSlot=eInvSlot_SecondaryWeapon) ), aStatProgression=((StatType=eStat_Offense,StatAmount=2), (StatType=eStat_HP,StatAmount=1), (StatType=eStat_Strength,StatAmount=1), (StatType=eStat_Hacking,StatAmount=5), (StatType=eStat_CombatSims,StatAmount=0)), )
+SoldierRanks=( aAbilityTree=( (AbilityName="RogueStealthBonus") , (AbilityName="IndependentTracking", ApplyToWeaponSlot=eInvSlot_SecondaryWeapon), (AbilityName="IsmsOnTheMove") ), aStatProgression=((StatType=eStat_Offense,StatAmount=2), (StatType=eStat_HP,StatAmount=0), (StatType=eStat_Strength,StatAmount=0), (StatType=eStat_Hacking,StatAmount=5), (StatType=eStat_CombatSims,StatAmount=0)), )
+SoldierRanks=( aAbilityTree=( (AbilityName="IsmsNBKMobility", ApplyToWeaponSlot=eInvSlot_PrimaryWeapon), (AbilityName="IsmsSoulCollectorB3"), (AbilityName="IsmsScoutIntel") ), aStatProgression=((StatType=eStat_Offense,StatAmount=1), (StatType=eStat_HP,StatAmount=1), (StatType=eStat_Strength,StatAmount=0), (StatType=eStat_Hacking,StatAmount=5), (StatType=eStat_CombatSims,StatAmount=0)), )
+SoldierRanks=( aAbilityTree=( (AbilityName="Evasive"), (AbilityName="RapidFire", ApplyToWeaponSlot=eInvSlot_PrimaryWeapon), (AbilityName="VitalPointTargeting", ApplyToWeaponSlot=eInvSlot_SecondaryWeapon) ), aStatProgression=((StatType=eStat_Offense,StatAmount=1), (StatType=eStat_HP,StatAmount=1), (StatType=eStat_Strength,StatAmount=1), (StatType=eStat_Hacking,StatAmount=5), (StatType=eStat_CombatSims,StatAmount=0)), )
+SoldierRanks=( aAbilityTree=( (AbilityName="IsmsLastWish"), (AbilityName="Faceoff2", ApplyToWeaponSlot=eInvSlot_PrimaryWeapon), (AbilityName="IsmsRelocate") ), aStatProgression=((StatType=eStat_Offense,StatAmount=1), (StatType=eStat_HP,StatAmount=1), (StatType=eStat_Strength,StatAmount=1), (StatType=eStat_Hacking,StatAmount=10), (StatType=eStat_CombatSims,StatAmount=0)), )

;taunt has damage immunity function. fix it.
; to fix bug, see mod page

As you can see, i've tried to "replicate" an alternate Gunnery Sgt Rank and pushed the original last rank to LW2's last (MSGT). This Rogue retains all of the unique Rogue perks (except marking one because now she has a holotargeter). Only common perks have been replaced by holo perks. You'll have very high chance too see and pick "common perks" in new LW2 AWC anyway :)
EDIT: Lastly, for a holo-user, she is only a "tick" worse from Holo Sharpshooter. (No Multi Targeting Perk in skill tree. ) Merely a small price to retain uniqueness.