I doubt it. Beside Kirk doesn't meet Khan until 8 years after events that take place in the up coming movie. Also, in Space Seed, they don't know who Khan was. On the other hand. If Kirk meet Khan some years before the events in Space Seed? Then it would explain how Khan got the delta badge.
I don't think that Space Seed is reference here. The events in the new timeline could mean that Khan was discovered many years ago, maybe by April himself and recruited instead of fighting him. So Khan could be OK and explained OK, as his ship was out there in space all the time, not appeared just when Space Seed happen. I really think that if Harisson is Khan than he was found by April ...