The BBEG should focus herself on discrediting the PCs. This, easily enough, starts with accusing them (correctly) of collaborating with a priestess of Talona.

A good way to do this is to have the BBEG send out an armed party, probably part of the city state's normal armed forces, or maybe even militia. The BBEG should arm these guys as best as he can, and possibly insure that several jerks are among the members. First, the PCs will see all the good 'loot', and will be predisposed to slaughtering the people trying to arrest them (the priestess of Talona probably won't be helping, not wanting to be hanged). If the PCs go along with the scouts, the BBEG simply tosses them into another dimension, poisons their food, or whatever.

If the PCs attack (which is likely--let the rogues or whatever detect the scouting party and hearing about how they're supposed to 'take care of' a bunch of well-armed folk--try to make it sound like they're 'in' on the plot but in truth they aren't), have your BBEG or her pet wizard scrying the scene. Since your bad guy should be rather powerful, given the stature of the PCs, it shouldn't be that hard to get someone in a high office, like captain of the guard, to be teleported to the scene of the massacre. If possible, the BBEG should scry it for the guy as well.

If possible, your BBEG should plant the body of a neighboring nation's soldier among the dead as well (this soldier should be disguised, but not in such as way as to make him indistinguishable--such as a partially cut off part of a legionaire marking, for example).

This will convince people that the PCs are dangerous murderers (especially in the scouts bodies are stripped, which they should be). Probably mercenaries from city X. The PCs are then publically humiliated and hated--which will probably guarantee that they'll never take control of the town except by force, as the stain of being branded a murderer is hard to make.

At this point, the BBEG has discredited the PCs, caused an uproar of public opinion (and possibly nationalism), and has grounds to conquer said neighbor. Possibly even an excuse to elevate herself to a high position, such as leader of the armed forces. After the neighbor has been crushed, with minimal losses, the BBEG discovers it's a conspiracy of nations. Her puppets in the council then nominate her to assume the mantle of high protector, or some crap like that. Basically, something that gives her more power than an individual councilman and opens the doorway for her to assume complete control of the city nation as a monarchy or dictatorship.

Considering the religious nature of some of the members of the party, the BBEG should send emmisaries to some of the churches. One of the paladin's, as she did murder several scouts in blood. Can always say she's fallen. Then, perhaps, send emmisaries to churches of justice/vengeance, possibly with a bounty, saying the vile evilness inflicted by party. Heck, put out a call for heroes against them.

The problem with your PCs lie in their high levels. There's not much they should fight that should give them problems. On the other hand, their total lack of spellcasting power means a mid-level batman wizard, with meatshields, can effectively shut them down.

On the other hand, if the BBEG makes it clear that the only way they're getting to her is over a mountain of corpses supplied by the time, the PCs may decide to go abroad to gather some support.