I'd rather not turn back the clock. Sure, there's some things that I'd do differently, but most of us have unallocated resources remaining and now is a dandy time to spend them to fortify against more surprise attacks. And getting a little more strict on the divination/teleportation magics will also go a long way towards stopping further magical assassinations.
An important one that a lot of people used seems to be the Mirror of Mental Prowess. It functions off of Clairvoyance, which has a range of Long (as opposed to unlimited in 3.0). So it can spy and open a portal, but it'll only go a few hundred yards. It also takes 10 minutes to cast, in the same way that Scrying takes an hour to cast. (Greater Scrying takes only a round and lasts an hour per level, but it much harder to get). It makes scouting creatures much more important if a stationary and invulnerable magical sensor can't be used to find every bit of intelligence.
Honestly though, I see some pretty good comeback strategies for evil that good doesn't really have at their disposal. Especially if they band together to ward their fortresses and battlelords.