I deliberately the first person in this post because this is what I do, but I don't imply that these are beads of universal wisdom. I posted this on a G+ thread earlier, but I meant to leave it somewhere that archives better than social media.
I don't try to keep PCs in a party. It is OK to let them explore parallel lines and coalesce whenever. This requires people happy to participate in the discussion event when their PCs isn't in the scene. Players also may take over antagonist for the duration of a scene and often turn out to be way nastier than if NPC'ed.
I use the FATE-like aspect approach. I make simple statements that players chose to deal with or not. Not dealt with aspect are guaranteed to be biting back at the right time. I dropped hints in my session report as to what was in before and after the session and you can see how the PCs dealt with them. Through their actions, I generate new aspects. This allows multi-step solution to complex problem, and give characters a lot of room to breath as far as story arc goes.
I use mainly the influence check as a mechanics to resolve conflict. I keep physical combat down to a few key event that have a critical impact on the campaign. When there is a combat, ask yourself what makes this situation unique and will challenge your player's GURPS mastery the most.
Players aren't PCs, I allow influence check against PCs and when they lose, the character has to act accordingly. This makes it easier for players to make sub-optimal choice without looking like dorks.
I think of characters as temporary threads into a bigger braid: they can come and go. There is more chance for them to be knocked out of the story than simply being killed. My players actually like to be able to jump into new characters to be closer to the main arc until the tide turn.
I am not a big fan of character point inflation. I'm cheap with them, but will allow to shift limited points (FATE-inspired move here), and won't shy away from granting expensive advantages (patrons, contacts, ads) wherever the players worked hard to get there.