Obsidian has already say there aren't any parallels between the NCR-Legion war and any real life conflict, at least not intentionally.
There doesn't really need to be any intention. The politics and intrigue behind both the NCR-Legion conflict and the real-life issues in the Middle East are stories as old as time, and similar events have occurred all throughout the past. It's easy to stumble upon this topic by pure happenstance, you could easily find similar narratives in plenty of other games. They're not rare.
It's just that there are more similarities because of the setting and contemporary technology. In New Vegas, it's a desert setting where most settlements have not progressed too well, and the Legion are poorly equipped insurgents that use guerilla tactics and terrorism yet possesses a large number of supporters and are able to effectively conquer whole lands. Their beliefs are in the service of one central being, and they are hostile, misogynistic, and xenophobic. To hammer the point home in the least subtle way possible, they try to bomb the monorail system of an airport.
But I guess the similarities rose from the fact that the NCR was trying emulate pre-war America in the first place, and the parallels ending up this way were likely from the start. Obsidian didn't have to try, just by thinking logically and being good writers that can simulate realistic events in their heads, the NCR would end up channeling real-life USA eventually. Hey, I wonder if the Legion won, would the NCR start supplying raider gangs to fight the Legion?
And to the OP, I was honestly expecting Bethesda to pick the Independent ending or have a WitW scenario. NCR ending being canon is actually a pretty good scenario.
The independent ending will certainly be the easiest for them, which means it's likely they'll be taking it if they were the ones choosing. The NCR ending would be pretty boring, it would be exactly like every other game ever. I never liked the Legion, but I would be more interested in seeing the results of their victory.