More train or more plane? (Longer train to Frankfurt vs an extra layover from Zurich to end a trip?)

JMHO, but the first option sounds like a royal PITA, especially if it involves getting a toddler up at 0500. With the second option, at least the train would be easier with a young child - you can sit around a table. You can walk them up and down the train if they are restless, it's just easier than train plus airport hassle plus flight. And you can still get a good night's sleep, and have breakfast before going to your flight.

I agree with CJean, the latter is the better option.

Sorry, but where are you starting from that is 2 hours and a train change from Zurich?

I'd absolutely do the Frankfurt option, but if you've already purchased your airfare you should consider that if you don't show up for the first leg of your flight there is a small chance they cancel your seat for your connection, especially if it's a full flight and they have people on standby. I'd be calling the airline to confirm that they won't give up your seats if you don't fly from Zurich. I haven't experienced this personally, but I've heard of it happening.

Go to Frankfurt.

Don't worry about the transfers. You basically have options every hour from everywhere in Switzerland to Frankfurt airport, so if you miss a connection you take the next one.
There is a HIlton and a Sheraton directly attached to the airport. From there you just walk to check in.
There are several more near the Gateway Gardens S-Bahn stop. If you book one of those just travel - Frankfurt, Gateway Gardens.

In your case, I would take the train option. If there is a problem with flights the morning you have to take yours, you could miss your connection. You also have to go through exit immigration and that can take time.

With all that travel, and a small child, I would take the least stressful option.

At Frankfurt Airport, there is a Marriott, Sheraton, Hilton and Hilton Garden Inn attached to the terminal. With restaurants all around. No need to even go outdoors.