Im not gonna pass judgement.....Im just gonna ask questions....
Why would Ashara allow them to use her baby in this scenario? Other babies are available in a timely manner.
Where does Rhaegar and Lyanna factor in?
What promise would Lyanna make Ned promise to keep?
Why would the Kingsguard be at the Tower of Joy? That would be a beacon of obviousness shining the light on something you wanted quiet.
Why is Ashara at Starfall when Ned returned a certain sword to her? Why would Ned treat the woman who killed his child with any sort of respect?
Ned and Ashara would have had to slept together at the infamous tourney of Harrenhal (for the timeline to make sense), that doesnt make sense with the anecdotal evidence we have from Jojens story....
Those are just the ones I thought of at first glance....Im sure Ill come up with more in a sec....
well -
to start with, OF COURSE ashara wouldn't allow her child to be killed just like that, it should have been done against her will, but see above for my actual theory. it would be interesting though to guess WHO substituted the babies and who KNOWS about that - i'll have to think about that. if q=a, those would obviously be doran, mellario - his wife... maybe somehow also alleras-sallera?
furthermore, ashara's baby was probaby kept secret (just like lyanna's), so it was actually convenient to use a baby that "never existed" - thus aegon could be safely sent away - there would be no baby lack, and no baby surplus, so to say.
if lyanna could keep her pregnancy secret, why not ashara? we simply don't know that much about her yet.
lyanna and rhaegar story isn't actually affected in any way by eddard-ashara story - until the moment eddard takes jon in as his son instead of his and ashara's own. everything about l+r=j still stands - the promise, the kingsguard...
somehow the fact that they both had secret children makes eddard-lyanna brother-sister bond even stronger.
as for the harrenhal tourney (it is actually meera's story, not jojen's) - i think it actually works in favour of this theory - we know that Ashara danced LASTLY with "the quiet wolf" - and we don't know what happened later. besides, meera's story isn't that anecdotal after all - she and jojen kept asking bran how was it possible that he had never heard that story from his father