You can remove the photo eye completely by replacing it with a 12v automotive relay. I picked up a 5-pin relay from O'Reilly and used it on my US Automatic Patriot 1. Wire the coil pins of the relay to the control board (pins 12, and 2 or 7). Wire the NO (normally open) pins between control board pins 7 and 8.
The photo eye itself contains relays that send a 5v or 0v signal to the control board pin 8. A 5v signal appears to signal that the beam has been crossed, where a 0v appears to be the "all clear" signal. The automotive relay simulates this behavior.
Edit:
I posted this and then forgot about it. Not a regular user here. As seen in photo, the pins that power the coils are attached to #12 and #2 on the board. I have then wired the normally open pin on the relay between #7 and #8 on the board. Nothing particularly special about the relay, it just happened to be the first one I grabbed off the shelf. Note also, that I'm using the "red" board. The pins and functions are likely different with the different boards.