We are flying into Malpensa and taking the train to Bologna, where we will stay. We have a connecting flight in Frankfurt, with a quick turn around time. Should we wait to purchase our train tickets when we get to Milan Central, in case we miss the connection, or keep fingers crossed and book ahead of time?
Wait and purchase once your flight has landed; too many things can go wrong.
Absolutely, wait until you arrive in Milan to buy tickets. The trains between Milan and Bologna will likely be high speed trains and the tickets are specific to train, date and departure time. If you miss the train you booked due to flight delays or whatever, the tickets are worthless and you'll have to buy more anyway.
From Malpensa you'll first have to get to Milano Centrale using the Malpensa Express. Note that there are two routes, one to Milano Centrale and one to Milano Cadorna, so be sure to board the correct train! It's also very important to validate your tickets for the M.E. prior to boarding the train, or you'll risk hefty fines!
I'm pretty sure you can buy both legs of the trip (Malpensa-Milano C.le and Milano C.le-Bologna C.le) at the Malpensa train station.
But yes, don't buy until your feet are safely on the ground at the Malpensa station.
There's plenty of trains between Milan and Bologna, no need to purchase in advance.