1. Download the Pack File Manager
2. Go into your extracted PFM folder and open the file "schema_R2TW.xml"
3. Scroll to the bottom of "schema_R2TW.xml", respect the formatting, add this schema, and save:
<table name='missile_weapons_to_projectiles_tables'>
<field name='missile_weapon' type='string_ascii' />
<field name='projectile' type='string_ascii' />
</table>
4. Now, launch the PFM and open the file "SpecialAbilitiesBeGoneV3.pak" (you'll find it in your Rome II /data folder, right?) Most of the file names and their contents should be self explanatory, but essentially, land_units_to_unit_abilities_junctions_tables is for controlling the special abilities of units; missile_weapons_to_projectiles_tables is where flame javelins once resided before I gleefully deleted them from the game; and unit_special_abilities_tables gives you control over a special ability's duration, cool down, etc.
5. Make your changes, save. If your game crashes/freezes while loading, you probably deleted something you shouldn't have (like that ability Second Wind). Don't fret. Go back to step 4, rinse and repeat until the game is playing to your satisfaction.
6. Enjoy.