Looks like the seeds for the Rogue's Code have been planted.
There is most likely an original timeline where Barry got his powers, by himself, and his mother is still alive. In the comicbooks there are timelines where Barry's mother isn't dead. She's only been dead in comics since around 2009 if I recall correctly.
We've seen from this ep that time will try to correct itself in some way. I'm assuming that lightning bolt would have hit Barry with or without the particle accelerator.spoilers:end of spoilers
It is also a possibility that they might make the bolt of lightning that struck Barry in the first episode "Barry Allen himself". Since in the comicbooks he becomes the bolt of lighting that gives himself his own powers.