Part of the problem wasn't that they couldn't move, it was that the power used to move them would kill them before they escaped. The trap used to counter their movements, or if it fails to do that, irradiate them to death anyway. The thrusters were used to reduce the amount of power the trap could used to irradiate them. The single boost to break inertia before the trap countered the effect, as they found there was a slight delay in the trap's reaction time, but it wasn't a lot. Their simulations were to use computer controls to rapidly change how they were boosting so the trap didn't have time to counter their momentum, but the energy usage would increase the radiation to the point it would kill the crew before they escaped....are at least it did in some of the simulations. That was why they didn't want to use the computer to do the run...not every simulation came out with them living, and for whatever reason, the slow human controlled run was seen as the higher chance of survival than the computer controlled run, due to the radiation caused by the power systems. The computer controlled run added more power to the trap's radiation field and reduced the time they had to live to a level that wasn't adequately simulated. Sometimes the computer could make it and sometimes it couldn't, possibly because their were too many variables in the field they were in. Moving rocks, moving parts of the trap setup in those rocks. And variable power needed due to theses shift causing a variable amount of radiation each run. One minute they might make it, but if they started a minute later, the factors could be too much and they'd die. With a human controlled run, the crew had at a known time limit for them to escape without getting even more rads thrown at them by their own power usage. It was still risky, but it had less variables that could result in their death than the computer run.
Also humans seem to like to put their possible deaths in their own hands rather than let it be something they can't predict. If the computer controls the whole run...they might make it, they might not...and they have no control if it start to not work....they just die from the radiation while the ship cruises out with over a thousand dead. Potentially leaving a Galaxy-class starship open for salvage rights to any race in the region.