In a nutshell you're proposing that lower level players will need enough commendations from higher level users to play with the "decorated veterans" of GoI.
I don't feel the commendation system would be reliable to judge a new player. Giving someone a commendation at the end of a match has become the new 'gg' in GoI. This applies for veteran players as much as for beginners.
Conversely, a few mean spirited players could keep out deserving new players, at least in the short term. But that may be enough for a few players to get fed up and drop GoI entirely. Which leads to my next point, I'm afraid this system would encourage elitism.
Sure, in theory Muse could implement all sorts of reporting systems to go after players who give out commendations to everyone or those who conspire against new players. You also mention investigating players and processing 'appeals'. To me that just adds too much complexity to the game. And as far as Muse is concerned they probably already have enough on their plate, they don't want to be playing hall monitor.
I'd approach GoI a bit like hockey: Call the penalties but let the players police themselves.
Personally, I love the anarchic and open nature of this game. It really fits into the post-apocalyptic "Wild West" theme of Guns of Icarus.