Sounds like a dog chasing its tail, trying to align switch reading while futzing around a 3 way.
Seems like sensing current going to the light would be pretty easy to hide.
Also I'm guessing you're using one of those jank hobby relays that constantly draw power the whole time the light is on. What you want for a safer, better setup, is a latching power relay.
And instead of having both the switch and the relay share light powering duties, let the relay do everything. Turn the switch into a switch on the Arduino and nothing more. You will always know what state the light is on without having to sense a darn thing. That's how I did it and it works fantabulously.