The Strength Penalty to Damage Remains Unadjusted
A Medium creature with Strength 8 who's fighting with two weapons, a longsword in one hand and a short sword in his off-hand, will inflict 1d8-1 points of damage with the longsword and 1d6-1 points of damage with the short sword, for example. The same creature with Strength 6 will inflict 1d8-2 points of damage with the longsword and 1d6-2 points of damage with the short sword.
From the SRD.
When you hit with a melee or thrown weapon, including a sling, add your Strength modifier to the damage result.
When you deal damage with a weapon in your off hand, you add only ½ your Strength bonus.
Wielding a Weapon Two-Handed
When you deal damage with a weapon that you are wielding two-handed, you add 1½ times your Strength bonus. However, you don’t get this higher Strength bonus when using a light weapon with two hands.
Also from the SRD:
A modifier is any bonus or penalty applying to a die roll. A positive modifier is a bonus, and a negative modifier is a penalty.
Emphasis--except in the headers--mine. Thus while the bonus may be different, the other kind of modifier--the penalty--is unchanged.