It seems that to deal with this problem something along the following lines is needed(IANAL):
When there is evidence that must be concealed from a suspected terrorist, they can be assigned to a tribunal rather than a civilian court. This assignment would be approved by a judge, not made unilaterally by the executive branch.
Persons brought before a tribunal will be entitled to an attorney, but not one of their own choosing. The attorney will be chosen from a list of attorneys cleared to access confidential evidence in terrorism cases.
These attorneys would probably be mostly or entirely government employees. They should have guarantees of independence, so they would not face penalties for aggressive representation of their clients. They would of course face criminal charges should they leak any confidential information.
Defendants would also be permitted to hire attorneys of their own choice, for general counsel and to call or cross-examine any non-secret witnesses.
Defendants wouldn't be allowed to examine the confidential evidence, although their approved attorneys would. In some cases, the defendant wouldn't even know the specifics of the charge. This is really straining the Sixth Amendment to the breaking point, but it seems almost impossible to get around this and still keep the evidence secret. The only alternative I can see is the Ashcroft plan to just lock people up without any judicial proceeding, which is worse.
Not only does this set up a dual-track procedure that emphasizes the rights of the defendant in regards to non-secret information (which is probably the fairest way to handle it) but it actually wouldn't be that difficult to implement. It's not as easy to implement as "lock up everybody that looks funny for life", of course, and therefore likely won't see the light of day any time soon, but if anybody becomes interested (or we have an administration change) the arguments work.
By the way, I'm aware that I was going to write about Brock today, but I've been somewhat consumed by the antics of the (more aptly named than I knew) American Taliban and the question of whether civil rights mean anything any more if they aren't convenient. I'll get back to Brock tomorrow, because it actually fits into these issues rather nicely.