Runner is moving from 2B to 3B on ball hit back to F1. F1 throws to F5 in order to make play on runner going to 3B. The throw to F5 causes F5 to cross the runner's base path (the throw took F5 to that spot). F5 catches the ball while in the base path as the runner collides with F5. The catch and collision occur at the same time. This also occurs a few feet from 3B. F5 tags the runner out, the runner who has been stopped dead in her tracks. Obstruction or Out?
Based on your description, no obstruction. The key to this is "the catch and the collision occur at the same time".
F5's position prior to receiving the ball did not cause the runner to alter her course to avoid her. Once F5 had the ball she can be anywhere she wants. If there was contact prior to F5 receiving the ball you have obstruction.