Most late-night shows participated in the strike initially, then were forced by the network to go back on air in improv mode. (Letterman was the exception -- his production company was able to make an independent deal with the union.) Stewart, Colbert, O'Brien, etc are all members (I think), but were also in the position of being The Boss. They all expressed near-nightly sympathy for the strike and lampooned the networks, but needed to continue to do the show so that the non-writing staff & crew could get paid.
MacFarlane can be disappointed in Stewart all he wants (and he's being goaded by Morgan, who clearly wants to stir up some shit), but he speaking from a much more privileged position of someone whose show is weekly instead of nightly, whose scripts are written up to a year in advance, and who works for a network that can replace his programming temporarily with Slut Island or whatever reality show some exec can crap out in five minutes. To say "I'm disappointed that you went back on the air while the strike was still going on" when it was obvious that wasn't what Stewart (or anyone else) wanted to do at all is to ignore the realities of their situations and the very real lives of the rest of the staff.