Im gonna have to say yes to your question, mainly cause it does say in the detailed description that it does take Modifer's that are affecting the opponent (both positively and negativly) into the calculation.

I did try to confirm this for you via the psypoke's damage Calc, but I couldnt find Foul Play in the Calc, Ill keep looking just so you can have a definative answer.

EDIT: Yes, I can say with 100% certainty: If your opponent's Attack stat is affected with a Negative Modifer, Foul Play losses it's effectiveness.

From the Pokemon Showdown Damage Calc :

+1 4 Atk Klefki Foul Play vs. 252 HP / 0- Def Abomasnow: 136-160 (35.4 - 41.6%) -- guaranteed 3HKO
-1 4 Atk Klefki Foul Play vs. 252 HP / 0- Def Abomasnow: 61-72 (15.8 - 18.7%) -- possible 6HKO

As you can see with Abomasnow at -1 Takes twice as long to KO than one at +1. (at -6 It literally says "worst move ever").
If you Plan on using Foul Play, I highly suggest you use it in conjuction with Swagger (if your using showdown rules, please keep in mind that swagger is currently in suspect testing).

One thing you forgot is that if the opponent is Burned, it will not lose attack power, however if the user of Foul play is burned it will cut the power in half.