For anyone having the same issue, I believe I solved the issue after some tweaking.
The issue seems to be that I wasn't setting pin 3 to be input before trying to read from it.
Adding the line os.system("gpioctl dirin 3") solved the crashing issue. Alternatively you could replace gpioctl dirin 3 with fast-gpio set-input 3.
I'm a little concerned that the error wasn't handled better. I don't know if that fault is on Python or my Omega2, though.
Anyways, happy coding everyone!