Unfortunately, blood biography combined with magical checkins and a spell-based binary search (probably using spirit planchets and generations of "retired" agents as spirits) to locate bodies spells doom rather cheaply as government spending goes.
Blood bio, cast with a drop of a ctreature's blood, gives answers to:
Who are you? (The name by which the creature is most commonly known)
What are you? (Gender, race, profession/role)
How was your blood shed? (Brief outline of the events that caused its wound, to the best of the victim's knowledge)
When was your blood shed?
Finding the corpse will have blood in its wounds, which then provides a "brief outline of events." It is reasonable to assume that a brief outline will discuss the method of attackers. Which then, (papers please!) will link them to the last internal checkpoint by their class descriptions or other characteristics linked to their identities.
To be clear though, the public side of things will be absolute silence. Because the public doesn't know about this appearance of weakness, there will be no advertising the weakness. (Otherwise people get the idea that harming the secret police is possible, and we just don't want that...) Reprisals are fine and all, but an aura of omnipotence is better. If the team missed any of its checkins or procedures, their supervisor (to the function of his ability to have fall-guys) will be tortured to encourage the others. If there are some rumors, some of the "usual suspects" will be rounded up and executed for a trumped up charge.
In terms of team notification, every team will, being lawful, likely follow "modernish" police practice of "check in with home base." The logistics of this vary, depending on infrastructure.
- Visible tech: A napoleonic semaphore is not out of the question, especially with items of "whispering wind." (Given how cheap this makes individual messages, combined with the efficiency gains from modern communications and the ability to spy on the communications of a populace, I see no reason why a lawful evil society wouldn't have one of these networks.)
- A wizard did it: Telepathic Bond may be made permanent. Every squad of agents should be placed in telepathic bond with their controller "back at base". Given the communications capabilities that this implies, it's the cheapest possible communications network. An "empire" (evil or not) lives and falls on its communications, which means that there should be a correspondingly high priority assigned to this. We can assert, however, that the idea of battle-ready flying squads ready to teleport to help requests may not be part of the repertoire, likely due to infighting and other politics. Still, even presuming that these aren't "always on" (maybe the controller is managing multiple squads) squads should check in when before they expect trouble and after they're clear.
The players get one missed checkin as a grace period, Then a "ministry of divination" (I'm assuming nation-state resources) steps in with a series of spirit planchettes and does a binary search to find the last location of the missing team (as a function of the region that they checked in from). The binary search only needs to be of a region the size that locate object (remember, both a corpse, the corpse's robes, and the identity documents marked with a specific arcane mark are all items) can cover. Happily, the players removed some of the evidence there, but a corpse is still an object.
That binary search takes exactly as long as you wish, as it's a function of the resources invested into the "ministry of divination"'s binary search capabilities and whether or not the "spirits in the area" are favourable to which side. Of course, if I was an lawful evil ministry of divination, I'd make sure that the spirits in the area were particularly well disposed to me: any spiirt that provides a useful answer has their family rewarded with a lowering of quota or other "random" bureaucratic positive outcome. Any spirit that obstructs this will a) have their family harmed, and b) be otherwise removed using normal mid-level adventurer capabilities.
If I was doing this in 3.5, I'd make sure that the communications infrasturcture all had the necrotic cysts implanted in them so that the parent-cyst could scry (and remote take over) any of her agents whenever she desired.
Best Answer
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.