Yeebo comments on my SWTOR beta post that he hopes "with the right mix of companions you won't be crippled without a dedicated healer in group content". I only spent a few hours in the beta and never got a companion, so I can't speak from my own experience. However, I did listen to NDA Roundup episode of the Darth Hater Podcast, where one of the hosts commented that he and a friend had successfully two-manned a flashpoint with their companions healing up to the final boss. They were unable to beat the last encounter because their companions stood in the fire and died.
The merits of the scripted "dance" of the modern MMO dungeon/raid encounter can be debated, but survivability of NPC "pets" have always posed a problem. Developers talk about how pet management is supposed to be a part of how you play a class that depends on having their pet alive, but it's hard enough for the player to get their own character out of the fire. MMO user interfaces seldom offer a reasonable option for micromanaging pets, companions, mercenaries, henchmen, and other allegedly helpful NPC's sufficiently to keep them from standing in stuff that is damaging them. Some MMO's even make pets immune to AOE attacks because this is the least difficult solution to this problem.
As someone who likes to do the occasional group content, I would love to be able to use an NPC to fill a tough-to-fill group slot. The problem is that so many of these "move out of the fire or die" mechanics are so demanding that there is no middle ground - either the NPC never dies in the fire and therefore is a more attractive group-mate than a human (who might screw up), or the NPC is useless because they always die in the fire. EQ2's always entertaining executive producer David Georgeson spins this as a feature - he claims that NPC's are intentionally designed to be less skillful than humans to preserve a role for other players - but the resulting NPC's will likely be worthless for the purpose that players have the most need for as a result.
(Aside: Mistakes made by the new EQ2 Mercenary AI are almost certainly increased by the fact that they're abruptly launching their expansion on a single week's advance notice, and less than a month after the start of beta testing. I see no way this can end well.)
Part of me wonders whether the solution is to take the specialized group roles that the overwhelming majority of players don't want out of the hands of players. That way, you're not balancing an encounter around a human tank and creating something too complicated for the NPC to handle - the NPC is the tank for the group, period, because players can't be tanks. There are definite downsides to this approach - I'm actually starting to like healing a bit, myself - but it does solve the tank/healer shortage. If MMO's continue to be predominately populated by DPS players relying on NPC's to do the support, it makes increasingly little sense to suddenly force that role on unwilling players at endgame.