While there was for some a lingering fear of more widespread destruction, the scientists on the project had calculated that this was exceedingly unlikely (though not strictly "impossible"). In fact, they were more concerned with the (far more probable) case in which the weapon would fail to work as expected and be underwhelming.

There were two different atomic bomb designs developed during World War II. One, the "gun-type" design that used highly-enriched uranium, was never tested prior to being dropped, for want of enough uranium to conduct a test and to use it in combat. The design was relatively simple in operation, and pretty easy to calculate the results of. It was also something that could be "almost tested" — you could experiment with assemblies of uranium that were non-explosive and would let you extrapolate what ought to occur when the full bomb assembly was created. They went into the summer of 1945 with confidence that the weapon when used would detonate with a power equivalent from 5,000 to 15,000 tons of TNT.

The other bomb design, the "implosion" bomb, was necessary in order to use plutonium as a fuel. It was far more complex and relied on many switches and explosives being fired with nanosecond-level precision, something which had never been done before. It was impossible to gain confidence in this approach without a full-scale test. For this reason, they detonated a test "gadget" in July 1945. Prior to the test, they estimated that the most probable explosive equivalent of the test was around 4,000 tons of TNT, though they also feared it could go much lower, down to the hundreds of tons of TNT or even less (which would be a failure, since it required around 4 tons of high explosives to operate at all). This was the one they fretted over and were unsure about.

But the Trinity test was much more successful than they had assumed, detonating with the violence of 20,000 tons of TNT. A gun-type bomb was used on Hiroshima with 15,000 tons of TNT, the upper-range of their estimates, and an implosion bomb was dropped on Nagasaki, with around 20,000 tons of TNT. So by the time they used them on cities, they already had a good sense of what it was likely to be, since they had tested one of them already.

That does not mean that they fully understood what would happen to the cities, what kinds of casualties there would be, and the number of casualties there would be. Their estimate for the bombing of Hiroshima prior to it taking place was that some 20,000 would be killed. In reality it was more like 80,000 on the day of the bombing and many tens of thousands more afterwards. They also did not fully predict how many radiation-related casualties there would be — they assumed that anyone in the (relatively close) range to be affected by ionizing radiation would have already been struck down by the (much larger) blast and fire effects. But the real world is often more complicated than the physicists' simplifications and estimations.

To get at your main question again, they were essentially confident that the atomic bomb would not destroy the planet when they tested it. But even on that point there was some uncertainty (their reasoning was necessarily indirect and there were several "unknowns" in their calculations), and there were certainly uncertainties about other aspects of the atomic bombs' usage. But they had a pretty good idea of what would happen.