Bit sad myself with the events in the latest book...The Starks do seem to have endured much sorrow and hardship!
As to the question at hand...Yes,Eddard was an honourable man..possibly too tied by his convictions to be Jon's real father..and that article certainly throws up questions...
Could also partly explain Eddard very strong stance against Daenerys being targetted for assassination..i.e knowing he himself was in effect harboring an heir of Targeryan blood...aside from the basic facts that it would go against his honour...Childslaying is not something I think Eddard would approve of..but,at this time both Dany and Jon are effectively adults!

Think part of me was hoping,in the early books,that Jon would end up marrying Dany...and restore peace to the kingdoms...unifying the Wildlings and the North etc.Maybe this can still happen..maybe?
Is there any precedent though for a sworn member of the Night's watch to actually be released from their vow..in a time of need/crisis..for the greater good etc.I realise they technically forswear their old allegiences and blood..but with Winter coming,and what it brings..seems to me that it would be more important for the watch to secure the aid of the north and the kingdoms beyond..by any means rather than let themselves and their charge be wiped out..because of an oath that could be bent.Who better than a Lord of Winterfell,allied with Stannis and potentially able to rally the North?
He may be a bastard but..surely,there are many Northern houses who would ignore such a thing..if it meant stability and the continuity of a Stark(whether it is in fact by true blood or possibly..as we see in this thread..a perception of such)..as the Lord of the North!

Jon Snows Ghost wrote:

In a SOS Catelyn described Jeyne Westerling as Pretty with good round hips (for bearing children). After the siege at Riverrun (AFFC) Jamie Lanister's description of the girl was different from Catelyn's. Jamie described her as being decent looking with Narrowhips and but not someone to lose a kingdom over. I take this as Jeyene being switched with her younger sister and the actual Jeyne most likely escaped with the Blackfish (Brynden Tulley). Jeyene's mother is actually playing her part in the deception.   Oh yeah this is just my theory and may not be true at all.

This is indeed an interesting theory. But wasn't the mother involved with the Lannisters in plotting the Red Wedding? That's why Jaime despised her.