It's still a pretty big quirk but I guess you could fix the client to warn about and correct the issue. You pointed out the fix...
Yep, you need purposefully spend both sets of coins to different addresses before a replay happens on the other network. I think I'd generate 2 new keypools too and redo my vanity if I started using it.
But I think it's easier than that. You just need to send all of your coins to yourself first. Doesn't matter which chain you do that on. That will split all your coins into their appropriate forks. From there you can spend them independently. The client could do this automatically for you the first time you use it. That would destroy all your coin age and maybe cost some fees.
The problem is that if you are not aware of it you are sending your alt-chain value to uncontroled addresses in an alternate universe, so the number of lost coins will be HUGE unless a large portion of the bitcoin ecosystem takes action at or around launch of the fork.
Fortunately, even if that happened "lost" LinearCoins coins would still be spendable. The BitCoiner would just have to come looking for them. Theoretically they still have valid keys.