Synergies.

[WarBlade]

I can't really think of any way to get synergies to work on this character class.

Which is curious considering you almost spelled out a pretty good starting point in your preceeding paragraph . . .

Their method was to take the uber-skills of previous versions and "nerf" their synergies (Nova, Frozen Orb, Thunderstorm, etc) so as to discourage their use.

That's where I'd start and I might be tempted to sever all ties between the timered damage dealers and the 'snap shot' skills too, depending on how the rest of the tree works out. By the looks of things, not even putting limits on the number possible synergies available to each skill will do much to encourage diversity, since the Masteries are already the default synergies to most of the rest of each tree and will always draw a player back to thinking the auxiliary skill would pick up the damage boost from that. However capping the available synergies for each skill to the grand total of one, will keep people to investing a maximum 60 points to a given skill, which might have some measure of influence in that area.

Multi tree diversity, as you rightly point out comes more from monster Immunities

How can you discourage one-tree Sorceresses in a way that makes sense?

Ouch, there's a pickle. It took me hours to make sense of the Paladin for the many various reasons involved with him and I suspect it would take just as long to properly sus out the Sorceress. With the Fire Tree it boils down to, Damage over time over area at whatever Mana cost, for each spell, constantly compared with every other spell. Lightning? More of the same with some added speculation on the functionality of Static, Teleport and Energy Shield thrown in. Cold is another kettle of fish full of its own similarities and differences with the other trees.

At a guess, I'd probably start by looking at diminishing returns Masteries and a synergy limit of one. At the very least I'd be reducing the 80+ point investments to 50-60 points plus pre-requisites and Warmth.