Short answer : Yes, you have to edit "main.cfg" in the Iguana's Tinker Tweaks config file.
Long answer : Yes, you have to edit "main.cfg" in the Iguana's Tinker Tweaks config file, but if you use tinkers tools instead of the vanilla tools you won't have to change the config. Iguana's Tinker Tweaks is made to add some difficulty to the pre-obsidian part of the game, so it disable vanilla tools. You can still craft the because its use in some craft like the Quarry from Buildcraft.
Here are most of the features the version 2.1.5 add to the game : (took from this post)
1. Tool Leveling
- Random bonuses on levelup
- Bonus modifiers on levelup
2. Pickaxe Mining Level Boosting
- Pickaxes start with 1 harvest level less, therefore have to be "mining leveled up" to reach full effectiveness
- MobHeads can be used as modifiers to instantly boost the mining level
- Exchanging the tool head removes the mob head and substract a bit of mining xp
3. Tool Part Swapping
- Allows to exchange a part of a tool with a new one
- Tool must be fully repaired to swap parts
4. Harvest Level/Material Tweaks
- New mining level Progression
- Changes Mining/Harvest Level of materials and blocks
- Adapts Tinker Tool Materials to the new progression (changes some stats). Mostly earlylevel materials.
- Creates a slower progression through the tiers (Wood < Flint < Copper < Iron < Bronze < Steel/Diamond < Obsidian < Ardite < Cobalt < Manyullyn)
- Emerald/Diamond Modifier only give durability
- Emerald/Diamond can be applied to a bronze pickaxe to increase its mining level to a steel equivalent! Without a steel pickaxe, this is the only way of getting to obsidian.
- Made from clay, must be burnt in a furnace first
- Can transport water, lava, milk and all TConstruct liquids
- Break when used to transport a hot material like lava
6. Various Tweaks
- Add Flint Recipe (Shapeless, default 3 Gravel)
- Remove Gravel Flint Drop
- Disallow Stone Tools
- Disable Non-TiC-Tools being able to harvest blocks. They can still be used for crafting this way. BonusChest Tools are replaced with tinker tools.
- Reusable toolparts in the Part Builder
- More expensive Silky Cloth, Silky Jewel
- Flux modifier takes 2 Modifiers
7. Part Restrictions
- The materials parts can be made out of are restricted
- All non-metals can only be used for a few parts
- Patterns have tooltips which parts are allowed
As you can see, most of those features are making a bit harder you progession into the game. If this is not what you want, maybe you should just remove the mod... You could also disable the modules that you don't want by editing the "module.cfg" in the Iguana's Tinker Tweaks config file. Finally, if you want every others features but that one, you can disable it by editing "main.cfg".