Ned knew the real deal
I think Lyanna probably told him after he found her at the Tower of Joy before she asked for her promise.
Afterall it seems that Ned bore nothing but respect for Rhaegar. Thats not exactly the opinion you would expect him to have of a man who he believed to have kidnapped and killed his sister.
I don't think Ned knew before hand though. He would've worked his arse off to prevent a war and as we saw in GOT Ned has no ability to work under the radar. Someone would've noticed and word would've gotten out.
The only reason its been able to be a secret for so long now is because both Ned and Howland Reed holed themselves up in their respective keeps and never left.
If Ned knew the truth there is no way he doesn't work to keep Brandon from going and while he probably wouldn't be capable of succeeding word would've spread like wildfire.
This post was edited on 9/28 at 7:20 pm