How do we know he was actually competent in that surgery? Yes, she said she couldn't tell a good smell from one that is foul, but I suspect Zoidberg "crossed the wires" metaphorically speaking. No, not intentionally, but as per his usual confusion about human anatomy, he linked the nerves to the wrong centers of her brain. It was just a happy accident his blunder resulted in a beneficial result (for both of them since she genuinely seemed to like him).
As for not dropping dead after, ahem, "spawning", I too thought about that. Maybe because she is NOT Zoidberg's species, she doesn't trigger certain hormones in John's body that would normally result in his death upon, er, "satisfaction".
One can choice to see it as contradicting earlier material, but I've opted to consider it as yet another level of "world building". Besides, I rather like Zoidberg and the poor schlubb deserves a break before the series ends.
Yeah, I'm full of crap. I might as well take a laxative.