This is an issue as well in "Final Mission," where the Enterprise is towing the radioactive garbage scow. The computer is counting down "lethal exposure in five seconds!" and in the nick of time the scow is released into the sun.
The way I rationalize it is this: the countdown specifically refers to the point in which hyronalin ceases to work. It's possible that hyronalin can only compensate for radiation damage up to a certain point, and then its efficacy drops very sharply. After this point, the chance of serious, lethal damage skyrockets. It's not certain that exposure will be lethal after that point, but every second or so past that point, the chance of lethal exposure rises exponentially. If the countdown hit zero, you'd start seeing everyone getting a spectacular tan, and then the usual radiation poisoning symptoms you are probably familiar with.
I have no idea how something like hyronalin works, but we barely even know how radiation damage works in the first place, at least yet. If the damage isn't instantaneous, but due to deadly by-products (like free radicals) formed by the radiation, it's possible that hyronalin could some how clean those out. There's of course a point where the damage would
approach instantaneous, and hyronalin would simply be too slow. Then, of course, you'd need really, really fast nanites.
Or, you know, metaphasic shielding. That probably would have helped.