I'm guessing they removed them because they appear on everyones Steam games list if they don't.

You mean achievements, right? Because we have pages for those. Their achievements were never removed though, as they were never added in the first place. I actually have talked to Jeff about this in the past and no solution came out of it due to the way Steam handles the games.
 
The problem is that those games aren't actually listed on anyone's Steam profiles as games that they own. The easiest workaround would be to check those achievements regardless, but then the player counts would be hugely inflated, and people who don't even own any Source games would have it on their list. There are two alternatives, neither of which I see as likely to ever happen. 
 
One option would be to have an opt-in for those games, allowing users to indicate that they play DIPRIP or America's Army 3 or whatever, and have the achievement updating system actually check for achievements in those games for users who have opted in. That would require additional options to be implemented on the interface, and since the developers seem to like keeping things super simplified that seems unlikely
 
A second, slightly more likely solution, would be to check the games people played in the past week. If they've played one of those free games then it will check for achievements in them. If they haven't, then there's no need to check for achievements.
 
So there are ways to workaround the problem. They'll just take a bit more effort.