Yes. It would have been a pain, but I did specify that I couldn't reject challanges and I wouldn't have gone back on that.
What happens if you knock Reshiram/Zekrom out anyway? In Black, I caught Reshiram with my third Ultra Ball on the first attempt, so I don't know much about the fight. I'm hoping it'll just restart that one fight, because I'll probably need to KO it and then capture it afterwards to progress.