I know it is a bit late to reply,
I spoke with a colleage of mine, and his experience with CMOS level micros and TTL level encoders came to a conclusion that as the pulses go by they do not draw enough current to cause any damage. I appreciate your explanation and simple logic but I want to share with you that on the Arduino DUE site,
Input and Output
Digital I/O: pins from 0 to 53
Each of the 54 digital pins on the Due can be used as an input or output, using pinMode(), digitalWrite(), and digitalRead() functions. They operate at 3.3 volts. Each pin can provide (source) a current of 3 mA or 15 mA, depending on the pin, or receive (sink) a current of 6 mA or 9 mA, depending on the pin. They also have an internal pull-up resistor (disconnected by default) of 100 KOhm. In addition, some pins have specialized functions:
Usually pull-up resistors are 10K, so if that is the case, the 0.11mA current is insignificant to the 6-9mA sink. What are your thoughts? As it stands, my board still receives the 5V pulses and the control seems to be just fine. My concern is what happens in the long run.