There are at least 2 episode coming up in season 4 which will address the athosians (eps 7 and 8)
It will be nice to find out what has been going on with them in all this time!
Also in reference to the thing about atlantis taking off without them, the athosians were actually relocated prior to atlantis taking off, they now reside on a place called new athos. Im unsure whether the full relocation happened at the end of season 1 or whether it was later on. The only shots there have been of new athos so far, however, were inside a tent when teyla and ronon were negotiating with the genii when sheppard et al come to pick them up to go off, save the day and reclaim atlantis, so it will be nice to see the actual proper planet!