I thinks it's an excellent idea. Apparently Gaun't Ghosts get a write up in Hammer Of The Emperor which might be of help when it hits the shelve.
Dan Abnett's books will be great for reference and inspiration and that link to the timeline will make you job easier in one way and yet harder in another, in my opinion.
Why I think it will be harder stems from that you are restricting your story to Gaunt's timeline. Should your story ever catch up to the curent time period or surpass it then you'll be treading into material that cannot sync up to the Ghosts as Dan Abnett hasn't written it yet.
Depending what is in Hammer Of Emperor you may have to come up with stats for what Dan Abnett has already created in addition to making up your own cast and places for your story. And then make sure that it all meshes together.
If anyone in your group has read the series then they may end up comparing what they see Dan Abnette's writing to the story your trying to tell.
Having said all that it would be amazing if it all came together - I have played in a game where the storyteller succesfully pulled it off based on an anime tv series.
The core rule book for Only War has a chapter on setting up an Imperial Guard game in there other gamelines that already have published material ready to be adapted into an Only War story. Thinking of the Jericho Reach from Deathwatch.
Heck the material on the Spinward Marches is a great starting point with several published adventures ready to go making a Storyteller's life much eassier
I wish you the best of luck on your endeavors though.
A final thought, when I was setting up my current game I asked the Players the type of game they wanted from the regiment they wanted to be part of to the enemy they would prefer to fight. We spent two nights building up regiment, characters, companions, NPCs. The story I wanted to tell changed a little based on the time spent with the group building everything up… Not that this was a bad thing. We even tok the time to build up the world and star system the Players came from by using the rules from Rogue Trader's Stars Of Inequity.