Yeah keeping Joanna McCoy's daughter and the Chekov love angle would have made sense. I wonder why they decided they had to drop Joanna entirely.
Maybe it was felt that having the character be connected to McCoy would overshadow her connection to Chekov, since McCoy was the more prominent cast member. Fontana's script would've mainly been about the Kirk-McCoy relationship, with Joanna as a catalyst. The final script was more directly focused on Chekov's relationship with Irina. And really, I'm not sure what the value would be in doing it as a McCoy-Chekov dynamic. Basically all you'd have there is McCoy in the role of the disapproving dad telling the boyfriend to have his daughter back by curfew. Since there's no established friendship between McCoy and Chekov, there's no more going on than that, so it's not as interesting as if McCoy's best friend is the one getting involved with his daughter.
Also, Heinemann was clearly more interested in focusing on Spock and his interaction with the space hippies. With Kirk vs. Sevrin as the A plot, Spock bonding with the hippies as the B plot, and Chekov and Irina as the C plot, there wasn't really any room for dealing with McCoy and his daughter.
I don't mean to doubt the OP but I think any script which has Spock killing McCoy's daughter (even accidentally) has to be suspect. I mean maybe it could be a first draft but could any writer be that naive?
No series could survive that (except maybe nuBSG). Did they have in the epilog that funny little banter they sometimes ended TOS ? McCoy laughing it off at Spock's expense?
Did they think that in the next week Spock and McCoy would interact normally?
Remember, this is '60s TV. Nothing
had ramifications in later episodes. Kirk lost his brother in one episode, the love of his life in the very next episode, and his wife and unborn child a couple of seasons later, and yet we never again heard another word about any of them. We even saw Mr. Leslie die in one episode and be back to normal in the next. Every episode was made to be a complete, self-contained story that could be viewed in any order relative to other episodes and perfectly understandable if you'd missed prior episodes.