one part would still make it to Atlantis
Not quite, things only go through in one piece, so the front half of the jumper would just disappear. Otherwise everyone could have just stepped through, and they could have waited for the gate to shut down, "only" losing the jumper in the process.
I'm sure that has been mentioned before that episode at some point, the rules aren't really consistent though. In S3E17 (A Hundred Days) Teal'c shoots a harpoon with a rope attached to him through the gate, which should not have hit anything on the other side until Teal'c makes it through the gate. I'm somewhat certain, that's not the only example of contradicting rules for the stargate 😁