It's a theory that I can easily see. Voyager is a very small ship for the exalted rank of full captain. I could see Janeway, with her background, as an officer being fast tracked to the admiralty. Voyager was a place to give her some ship time and a mission which was perhaps relatively easy. It would have made a great contrast with Chakotay, someone who'd commanded ships for real for some time at odds with a captain who was a rear echelon paper pusher. I guess they backed away from that or didn't see it that way, but it would have been a great conflict generator.
Considering her adventures included stranding her crew a lifetime from home in order to (very temporarily) help the Ocampa, being transformed into a warp 10 salamander, having to single-handedly save the ship from supersized viruses and being Borgified, I think a little psychological scarring is to be expected.
I was getting ready to type just that until I read your comment! Even better would have been to have the captain in some kind of coma instead of being killed while Commander Janeway took over. In year 2 or 3 he comes out of his coma and after evaluating the situation decides they should find a planet and settle down instead of continuing on the unrealistic journey to the alpha quadrant (his opinion). The story could go on from there. Maybe the captain is eventually killed and Janeway takes over again and continues on to the AQ while some of the crew stay behind on the planet.
That kind of conflict would be interesting, especially if Janeway had spent two years pep rallying everyone to believe in their ability to get home and then BOOM.. the Captain wakes up and says fuck it, we are parking HERE.
But even if she was orignally the first officer she still would have been the Captain after the death of the Captain. From a characterisation point of view it might have worked better, and the orignal CO could still have been a woman.
But then we would have almost had a female captain and a female CO and it would have been tragically ripped from us by DEATH and that would have sucked.
Kate did a great job with the material she was given. Janeway was potentially much more interesting than she became, eventually. The supposed novelty of her being the first female captain leading a STAR TREK television series never had any real hype, as far as I was ever concerned. After Princess Leia in STAR WARS, It's all kind of been done, as far as bossy chicks in Sci-Fi calling the shots. And even she's kind of overrated! But you know what? I always believed in Janeway, as a character and I never questioned her casting. I just wish that Berman had gotten a memo, relatively early on saying, "we have an interesting premise with this show - let's really try to push it and take some risks." That Berman kept control of STAR TREK for so long both baffles and disappoints me. It wasn't a "poor" captain in this series. It was poor leadership on the production end. By this time, Berman had lost his "stuff."