Now, if we deviate from canon from the very start, I wonder when would be best. If Duncan were a mage I'd suggest him personally stumbling upon Grail Works, and if we used a Mage Origin Grey Warden we could have him/her accidentally finding Grail Works during their Harrowing. Or, I suppose any mage or demon finding Grail Works could be a start. But if Jeanne is sent there without a contact, then I rather like the idea of her charging headfirst into the battle at Ostagar and, while not saving the day, certainly saving quite a few people (including Duncan). I'd say not Cailan, but the point of Grail Works is to save everybody. Him living completely alters the plot though. Duncan surviving doesn't help all that much in the big picture, even if his reputation does make life much more convenient. Plus, Jeanne saving him at Ostagar means she doesn't necessarily become a Grey Warden.
Honestly, if she's going to make an impression of a heaven sent angel, slaughtering darkspawn, being immune to the taint, and curing the survivors is a pretty damn strong impression. The problem is that what kicks of the DA:O plot is a tragedy and it would be well within Jeanne's power to prevent it. Maybe Cailan survives, Loghain deems him an imposter, and sparks a real civil war? Cailan going through hero worship for Jeanne is rather appealing, especially if with Loghain's betrayal he starts to consider her a potential bride.
The more I think about this, the more I think Jeanne saving the day at Ostagar despite Loghain's efforts is the right way to start the story regardless of how she's initially introduced. It's the tone appropriate to Grail Works. There are still ways to split the party and cause trouble. Revelation is an easy way to make the story work however the author(s) desire. Jeanne goes to the Arl while Duncan appeals to the Circle? Now Jeanne has additional reason to rush to the Tower where people not effectively immune to magic are, so she can save the day and get the help she needs. Say she can't completely exorcise the demon because the desire demon was let in with the blessings on the Arl's son, even though Jeanne is capable of suppressing the demon. Things like that.