The Civil war, the elven rebellion, the Breach, the mage/templar war. Orlais, if it survives as a nation, will not have much strength left at all when all is said and done.
And yes, the elves would have to pool all their resources and unite, and it would not be easy, but I do think it is possible.
And since when did human soldiers, or any soldiers for that matter, have to agree with their commander? Desertion usually means execution if caught, and betraying the only person in all of Thedas who can close the breach doesn't seem to be very smart. Especially if the Inquisitor happens to be Dalish.
You make a good point about the state of Orlais. That's a whole lot of crises to be hit with simultaneously. There is also the possible schism that Petrice mentioned in DA2 to consider, so Orlais's days may be numbered... it is possible that this war will end with the nation divided in half?
Regardless, the elves have a difficult task in front of them. Not only are the clans scattered across the continent and disorganized, they lack any reliable means of communication. I was thinking that perhaps the Eluvians could be used to quickly bring the clans to a single location, but the success of this plan would be dependent on how many functioning Eluvians exist and how quickly this technology can be made available to each clan... Although they will be preoccupied with the civil war, I have no doubt that the Orlesian military will take steps to prevent the elves from streaming into the country once they are noticed. Tbh, this all sounds very difficult to pull off, and the elves are on a time limit as well... The plan also seems too dependent on luck, chaos, and poor judgement on the part of the humans. If the Orlesians decide to deal with the alarming number of elves crossing their borders and heading for the Dales rather than continue fighting one another, things could go very poorly for the elves...
As for your final point, I feel that if the Inquisitor relies too heavily on their unique connection to the Fade to secure the cooperation and loyalty of their soldiers and political allies, they will most assuredly be overthrown shortly after the Breach is sealed. Once the crisis has passed, there will be nothing preventing the Inquisition soldiers from going home. If that happens, they might seek to join the armies of their native countries in order to reverse whatever military actions they were forced to participate in under duress... Since this is a voluntary army, I think that the only way to keep this group together in the long run is if the soldiers feel as though the Inquisition's goals match their personal ones... otherwise, the Inquisition will last only as long as the Breach does.