The solution to my problem was to put the following in my .i3/config:
assign [class="com-mathworks-util-PostVMInit" title="^Fig"] 2
This makes all Figure windows from MATLAB appear in workspace 2. The string "com-mathworks-util-PostVMInit" is the class name of the MATLAB figure which I found using the xprop terminal command.
To make sure that it's only the figure windows in MATLAB that's behaving this way I've also added title="^Fig", to seperate from other MATLAB windows.