The helium leaks weren't and still aren't an issue for the mission. They are an issue that should be addressed in the future, but they pose no safety risk as things currently stand. While Starliner is docked, it won't even be leaking any helium. The tanks are sealed shut when they aren't in use, and since the leaks aren't on the tanks themselves, they aren't losing any helium as long as they stay docked.

The thruster failures are also not necessarily related to the leaks. They don't know why the the thrusters shut down, but they were shut down in software and not due to some piece of hardware failing. Their current goal is to figure out why the software shut them down, and why 4 of the 5 that shut down were able to be restarted without issue. They aren't just assuming it can maneuver either, they know it can because the thrusters aren't broken. It didn't require any physical repair work to get them firing again, it took a restart.

Remember, this is just a test flight, and nothing that's happening is outside the scope of the test.