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Here's what the block responsible for skills looks like. To remove a skill, it's enough to make it so that it never drops. To do this, in the SkillType field we set SKILLTYPE_SPECIAL_PERK, in HeroClass we set HERO_CLASS_NONE, and in SkillsPrerequisites we remove all Item blocks. That should help.

		<Item>
			<ID>HERO_SKILL_BARBARIAN_ANCIENT_SMITHY</ID>
			<obj>
				<Texture>
					<Item href="/Textures/HeroScreen/Feats/Knight/DestructiveMagic_AncientSmithy_grey.xdb#xpointer(/Texture)"/>
					<Item href="/Textures/HeroScreen/Feats/Knight/DestructiveMagic_AncientSmithy.xdb#xpointer(/Texture)"/>
				</Texture>
				<CommonTexture/>
				<NameFileRef>
					<Item href="/Text/Game/Skills/Common/DestructiveMagic/AncientSmithy/Name.txt"/>
				</NameFileRef>
				<CommonNameFileRef href=""/>
				<DescriptionFileRef>
					<Item href="/Text/Game/Skills/Common/DestructiveMagic/AncientSmithy/Description.txt"/>
				</DescriptionFileRef>
				<CommonDescriptionFileRef href=""/>
				<SkillType>SKILLTYPE_SPECIAL_PERK</SkillType>
				<HeroClass>HERO_CLASS_NONE</HeroClass>
				<spellBuffs/>
				<BasicSkillID>HERO_SKILL_SHATTER_DESTRUCTIVE_MAGIC</BasicSkillID>
				<SkillPrerequisites>
					<Item>
						<Class>HERO_CLASS_BARBARIAN</Class>
						<dependenciesIDs>
							<Item>HERO_SKILL_CORRUPT_DESTRUCTIVE</Item>
							<Item>HERO_SKILL_MIGHT_OVER_MAGIC</Item>
							<Item>HERO_SKILL_POWERFULL_BLOW</Item>
						</dependenciesIDs>
					</Item>
				</SkillPrerequisites>
				<AIRacesValues>
					<Haven>
						<CommanderValue>0</CommanderValue>
						<CollectorSupplierValue>0</CollectorSupplierValue>
						<FreelancerValue>0</FreelancerValue>
					</Haven>
					<Sylvan>
						<CommanderValue>0</CommanderValue>
						<CollectorSupplierValue>0</CollectorSupplierValue>
						<FreelancerValue>0</FreelancerValue>
					</Sylvan>
					<Academy>
						<CommanderValue>0</CommanderValue>
						<CollectorSupplierValue>0</CollectorSupplierValue>
						<FreelancerValue>0</FreelancerValue>
					</Academy>
					<Dungeon>
						<CommanderValue>0</CommanderValue>
						<CollectorSupplierValue>0</CollectorSupplierValue>
						<FreelancerValue>0</FreelancerValue>
					</Dungeon>
					<Necropolis>
						<CommanderValue>0</CommanderValue>
						<CollectorSupplierValue>0</CollectorSupplierValue>
						<FreelancerValue>0</FreelancerValue>
					</Necropolis>
					<Inferno>
						<CommanderValue>0</CommanderValue>
						<CollectorSupplierValue>0</CollectorSupplierValue>
						<FreelancerValue>0</FreelancerValue>
					</Inferno>
					<Fortress>
						<CommanderValue>0</CommanderValue>
						<CollectorSupplierValue>0</CollectorSupplierValue>
						<FreelancerValue>0</FreelancerValue>
					</Fortress>
					<Stronghold>
						<CommanderValue>0</CommanderValue>
						<CollectorSupplierValue>0</CollectorSupplierValue>
						<FreelancerValue>0</FreelancerValue>
					</Stronghold>
				</AIRacesValues>
				<PresetPrice>0</PresetPrice>
			</obj>
		</Item>