I will venture to say no, you cannot use the 3-way switch to split the pickup.
From my understanding, EMG 89 pickups are actually two individaul pickups housed in one humbucker sized casing. There is a side-by-side double coil humbucker and a stacked coil "single coil pickup" neatly arranged and connected to a miniature pre-amp sealed inside the casing.
The push-pull switch actually activates the humbucker or the "single coil" and at the same time assign the pre-amp to whichever pickup is selected. Hence, the two pickup modes do not share the same coils or magnets. The only thing they share is the same pre-amp.
In this instance, the pickup split switch has to have 2 rows of lugs (a Double pole double throw switch). One row to activate either the humbucker or "single coil and the other row to assign the pre-amp to the pickup activated.
However having said that, there are various so-called Super Pickup Switches in the market which may allow the coil splitting capabilities for EMG89s. Do explore this option.