I think its a good idea for a story, but I'm not sure for Superman. Personally, I don't like the idea of taking away him being raised by Jonathon and Martha Kent and having him raised by the military. I think that would significantly alter his character, as his human "essence" has always been rooted in him being raised by human parents. If he were raised like a guinea pig by the military, I wouldn't expect him to come out of it with the conscience and love for humanity that Supes has.
But like I said, its a good idea for a story, as it offers the opportunity to sympathise with an abused, innocent and benign alien as it grows up only knowing a captive life surrounded by a different species. I'd change the characters and go with a totally original sci-fi story, instead of a Superman story. It has potential - and you could actually try pitching it to studios!