The ship's scanners had told Khan how violent Honides' weather was. The winds at that altitude could almost lift cars, and the metals they carried made them dangerous for the engines.
That quality only involved specific gales. Honides wasn't as plain as Nippe 2. It had many elements and features, especially in its atmosphere.
According to the scanners, the ship only had to descend a bit more to get past those metallic winds. A hundred meters would have been enough to bring it into areas it could cross. However, going against that initial layer would create a threat that Khan couldn't afford.
Ordinary soldiers would have to wait for the surface to send special ships or for the weather to calm down. Even Khan would have opted for those approaches under normal circumstances. Waiting wasn't a big issue, all things considered, but that would go against his main goal.