Petrified is a condition, like sickened or poisoned. Many spells can remove harmful conditions — Greater Restoration lists petrification. It is currently the only one, short of Wish.
Wish can either emulate Greater Restoration directly (its "duplicate a spell" functionality), or as part of a greater effect healing all hit points and removing all conditions that Greater Restoration can, on up to twenty creatures all in one go (at some cost to the caster).
As a spy, you presumably have a lot of deception-related skills. One good option is to make it look like a suicide. People who commit suicide generally don't want to be resurrected, and won't come back if you try. If you also create a fake corpse (find someone who died of old age and thus can't be resurrected, and disguise their corpse as the sorceress's), the sorceress's allies might simply cast raise dead, confirm that it failed, and give up.
Likewise, as a spy, perhaps you can impersonate the cleric who's going to be casting the true resurrection, and just tell her allies the spell failed. Heck, perhaps you can just impersonate the sorceress for a while, and tell her allies you're going on a personal side quest and please don't bother her for at least a year. That should throw them off the trail.
The problem with all the above approaches is that, if the sorceress is a player character, and the player is sitting next to you at the table saying "he totally killed me, don't fall for the deception", the other players might choose to have their characters not fall for the deception.
So let's talk about incapacitating her. One funny idea might be to capture her and put a helm of opposite alignment on her head. You can keep removing and re-equipping the helm until she rolls a 1 on her saving throw. Once she changes alignment, she might become your secret ally. (This is arguably the nicest thing you could do, in that it doesn't involve removing another player's character from the game.) Even if she doesn't become your ally, she "views the prospect (of returning to her former alignment) with horror", which means she probably goes into hiding to keep her former allies from changing her back.
Along the same theme, if she gets turned into an undead, it's impossible to resurrect her until the undead is destroyed. For example, if you let a wight or shadow or mohrg or spectre or vampire or wraith kill her, she'll become an undead and the true resurrection spell will fail. The problem with most of these approaches is that the sorceress's allies can just cast discern location to find the undead she's turned into, then teleport and kill the undead, after which true resurrection will work as normal. So it's a speed bump, but not a permanent solution.
There is one exception: if you let a vampire kill her, she keeps all her class levels when she turns into a vampire. This could make it very difficult for the party to track her down and kill her -- for example she could plane shift to somewhere they couldn't get to easily, or she could teleport away when attacked, or she could just fight them and be really hard to defeat. If the vampire that kills her has 10 hit dice, it gets control of her, and it could command her to run and hide, or to be your ally or whatever. Otherwise she's free-willed, which could be bad for you.
A third option might be to try to get help from the people you're working for. You've told us that you don't have access to a trusted spellcaster, but surely a whole enemy nation has at least one or two good casters? You might try incapacitating the sorceress and giving her body to your allies, and let them deal with keeping her prisoner.
Best Answer
Altogether, it's likely easier to bring back from the dead a petrified-then-broken creature than originally thought.
Can divination spells target a petrified creature?
Treating the resultant statue as anything other than an object quickly gets weird. Pathfinder creative director James Jacobs in this 2014 Paizo messageboard post originally agreed that petrification created a "mindless, inert" stone creature until it was pointed out that such a "creature" could still be targeted by, for example, the spell baleful polymorph and transformed into… a stone statue of a bunny? A living bunny made of stone? A real, live bunny? So, less than three hours later, he changed his mind: for playability it's better to treat a petrified creature (or at least a creature affected by flesh to stone) as an object, the spell's rules-as-written to the contrary.
In short, unless the GM rules otherwise, treat petrified creature like any other object with regard to divination and other spells. (So, for example, it's immune to the scrying spell but can be the subject of the shrink item spell for convenient transportation.)
At what point is a petrified creature considered dead?
James Jacobs in this 2015 Paizo messageboard post says that a petrified creature's "[d]eath occurs the instant [a] fatal breakage occurs."
What happens if the petrified creature is made into small pebbles then scattered across the land or the planes?
Right there. See that? Now that is a fatal breakage.