Chronomancer defined supporting in GW2.
In the last balance patch it was able to sustain every boon in the game including powerful, more rare boons like resistance and stability. Supporting in GW2 is not something that is seen as satisfying or fun by the vast majority of the player-base. I disagree with OP's core statement, "How do you balance Chronomancer?"
... Instead, I think the more relevant dilemma facing GW2's player-base is thus: "How do we make supporting fun?"
In my opinion DPS players have gotten a zero-responsibility pass for supporting for too long. I think supporting, what I consider one of GW2's core gameplay thematics, needs to return as a global responsibility. I think that if you want to play compositions that scale with boon quantity then everyone has a responsibility for general upkeep and respective support or boon-generation capabilities.
For example:
I think that by reducing the burden on "dedicated support classes" the game will become more engaging. Players will still have access to more boons than they do currently. However, skills will likely have to have their baseline cooldowns and effects adjusted. I don't think that it's healthy for every "boon-support" class to need 100% boon duration -- and I think that there are better, more fun ways to keep players busy in an active combat system like in GW2. I think that dedicated support builds should be rewarded, but I think that overall responsibility should be distributed amongst an entire group of players creating new support roles and responsibilities.
I think the problem with the last patch is that it very much did feel like half a balance patch. It took power away from Chrono, but didn't re-distribute practical boon application amongst other classes (or even boost Firebrand or Renegade to occupy the void). Lots of the more supportive traits in other classes are in obscure trait-lines such as Alchemy or Tools in Engineer and are designed in an archaic, irrelevant fashion that predates the existence of raids and dedicated boon-roles (or support classes). I think that many traits should be made ten man as five man traits have little place in raids at their current power levels (especially amongst dedicated supports).
Anyway, those are just some of the thoughts that have been mulling in my head for the past week. I've been playing support Renegade in Fractals for the past few days, and while I enjoy it to some extent, it has definite limitations in that it's clunky, exhausting to play and boon support is really all I'm doing -- different, but still tedious and not as fun as Firebrand. I don't really want to waste time arguing prospective changes so much as just lay out my thoughts on Chrono, Boons & the "support meta".