In the answer below I use the phrase teleportation ambush to refer to the following tactic: Group A uses a scrying effect to determine Group B's status and location. Then, if Group B is vulnerable and accessible, Group A prepares for battle and uses a teleportation effect to mount a surprise attack against Group B. Also known as scry-and-die, this tactic can devastate PCs, NPCs, the DM, the players, and the campaign. I've yet to meet anyone who likes staging or experiencing teleportation ambushes, but the tactic is so easy—and the means, like Hawthorne's birthmark, so deeply rooted in the game's foundation—that banning it outright as a tactic usually isn't an option.
My campaigns' assumptions…
In my campaigns, high-level PCs typically are not victims of teleportation ambushes because they learned much earlier in their careers—perhaps before the campaign even began—both that teleportation ambushes can occur and that they should acquire the means to deal with them.
If mentors don't explain to their apprentices before the campaign begins that teleportation ambushes are a thing, when apprentices become adventurers they may learn that teleportation ambushes are a thing alarmingly early on.
A level 7 wizard (or cleric with the domains Knowledge and Travel)—a difficult challenge for a party of level 3 PCs—can launch a deeply ersatz teleportation ambush from over 1/10 of a mile away using the 3rd-level Sor/Wiz spell clairaudience/clairvoyance [div] (PH 209-10) and the 4th-level Sor/Wiz spell dimension door [conj] (PH 221).
A level 10 wizard (or cleric with the domain Travel)—a difficult challenge for a party of level 6 PCs—can launch a for-reals teleportation ambush from a thousand miles away using the 5th-level Sor/Wiz spell scrying [div] (PH 274-5) followed by the 5th-level Sor/Wiz spell teleport [conj] (PH 292-3).
Encounter difficulty is as per the Dungeon Master's Guide, which also says that as many as 15% of PCs' encounters may be difficult (49). Note, also, that these casters can do this once per day.
When I design a campaign, I assume casters did do this once a day until folks figured out how to thwart them. Afterward, teleportation ambushes still happen, but they happen rarely and only in unusual circumstances. That doesn't mean, however, that folks get complacent about the possibility, but it does mean safeguards have been put in place to prevent the casual murder of civilized folk via teleportation ambushes. I mean, if there aren't safeguards against teleportation ambushes already in place when the campaign begins, I, personally, don't know how to maintain the campaign's verisimilitude. In short, I make sure my campaigns thwart teleportation ambushes (and the shadowpocalypse!) first and then I figure out the rest.
I address how to deal with scrying effects in another answer and how to counter teleportation effects in another answer, so I'm not going to rehash those answers at length here except to say that I think, in a typical campaign, the DM should prepare the players for the possibility that their PCs will be, at some point, the victims of a teleport ambush early in their careers so the players can be told by the DM how the campaign prevents teleportation ambushes or so the PCs can determine in the campaign how to deal with the tactic.
My point is that I—and just me, you totally might not, and that's okay—see the sudden introduction at high levels of teleportation ambushes as unfair. Since teleportation ambushes could've been a thing as early as level 3, I would feel I'd done the players a disservice by refraining from using teleportation ambushes when the tactic became available but then springing teleportation ambushes on them after the PCs assumed teleportation ambushes don't happen. That is, by introducing the players to teleportation ambushes earlier—when the game isn't quite the rocket-tag it is at high-levels—I give the players the opportunity to figure out how to deal with them. And they do.
See, in my campaigns, I make it clear from the outset that many walls incorporate thin sheets of lead, some places have permanent Mordenkainen's private sanctum effects, many places have hallow effects tied to dimensional anchor effects (which allows teleportation effects to be used to enter the warded area but not to exit the area), a few places even have password-protected forbiddance effects (far stronger and pricier than the previous combination!), and "[a]reas of strong physical or magical energy" litter the landscape… all so important folks, the rabble, and adventurers can live (relatively speaking, anyway) safely and fearlessly. And, as older protections fall into disuse or disrepair, important folks enlist those who can to make more defenses. Otherwise I imagine their fragile civilization collapsing.
So, yes, I encourage my players to have the party early on acquire a means to detect scrying sensors; to employ the 3rd-level Sor/Wiz spell anticipate teleportation [abjur] (Spell Compendium 13) et al., whether by spell, wand, eternal wand, minor schema, or whatever; and to overnight at places with lead-lined walls or possessing "strong physical and magical energy." In my campaigns, Can I hinder or prevent a teleportation ambush? is just one more thing an adventurer worries about, like Can I hit an incorporeal creature? or What do I do if I contract mummy rot in the middle of nowhere?
Accuse me of lacking imagination all you want, but I just can't imagine a campaign world using the typical D&D 3.5e rules existing any other way.
…But your campaign may vary (and, honestly, so do mine!)
In a current campaign I've made a house rule that says that bodies of water sufficient to appear on the campaign map prevent teleportation beyond them, forcing folks to cross rivers and oceans conventionally, and in a previous campaign spooky mists prevented teleportation beyond the valley that was at the center of the campaign. In both cases, the goal was to limit (not eradicate) the utility of teleportation and to mitigate (not dispense with entirely) the possibility of teleportation ambushes.
So I really, really don't want to make it sound in that overlong section up above like I'm somehow mandating that my way is the One True Way to play or anything. It's not. Seriously, I really can't know how your campaign handles teleportation ambushes—by strict reading, house rules, a gentlemen's agreement among players, a gentlemen's agreement among wizards, or whatever!—, but I do recommend that sooner rather than later that every campaign somehow addresses teleportation ambushes.
Note: I made the Comment mentioned in the question.