I'm trying to make my overall campaign pretty dark and have personal quests that are difficult and dark as well--I took inspiration (though not any actual stories), from some of the things I've read from the things that you have done with (and to) your players on this thread: http://greenronin.com/phpBB2/viewtopic.php?f=33&t=10557
I posted my ideas in that thread if you want to see them.
On Topic: Splitting the party is never an easy decision, but I learned early in running games, that allowing the players to choose was always the best policy. Whenever I tried to steer players to lead them to where I
wanted them to go, things didn't work as well and players would sometimes get frustrated because it felt like I was controlling them
, not the other way around. I think having two difficult and pressing objectives presented to players and having players choose how (and when) to approach them is a great tactic though. Just like real life, you can't tackle multiple things at the same time.
Putting them on a time frame isn't a bad thing either necessarily. You can only do one or the other--not both, while frustrating, is more true to the spirit of the game in a lot of ways. Maybe the super bad villain gets away yet again, but that doesn't mean they can't catch up to him eventually again. It's always a hard tactic, because it's great to have a recurring enemy that really gives the players a hard time--but if it drags on too long players get frustrated.
As Zapp mentioned though there isn't anything wrong in letting them split up and try and tackle both--but don't tone down the encounters. Perhaps instead of killing them outright however, you can allow them to retreat or get captured and create even more problems for the others. My only issue with PCs splitting up is allowing equal time to the different groups and tracking everything they're doing. PnP RPGs are complex and sometimes players forget how difficult it is to track every damn thing their characters are doing...