You're doing it wrong if your service generates thousands of dust-sized outputs. You need to consolidate your outputs as you go.

I assume that a transaction under your current model is like this:

Input (x1): 
Payer Address (X BTC)

Outputs (x3):
Payee Address (Y BTC)
Service Wallet Address (100 satoshis)
Payer Change Address (X - Y - 0.00000001 BTC)

What you should do is to keep the Service Wallet Address accumulate the 100 satoshis as you go:

Inputs (x2):
Payer Address (X BTC)
Service Wallet Address (Z BTC)

Outputs (x3):
Payee Address (Y BTC)
Service Wallet Address (Z + 0.000001 BTC)
Payer Change Address (X - Y - 0.000001 BTC)