You may have to contact Steam Support themselves, rather than use the Steam Refund system, since they may simply throw it out if you've played more than 2 hours.
Or maybe it will go through the refund system anyway. I got a refund today for a game I just purchased that had over 2 hours, because I explained that the game was broken and most of my time played was spent trying to get the game to play.
So, just because it comes up with a cross saying you're not eligible for a refund doesn't mean you can't submit a request anyway and include the relevant information.
But I don't know if they will do partial refunds, which you want, via the refund system. So I would still contact them through Steam Support first. That way you definitely keep the game in your library. Otherwise, it may be taken out, and you have to wait a week before you can reuse the funds.