While I'm sure there's stuff I haven't thought of, I imagine this wouldn't be too difficult to do with this setup. You'd want to change the victory conditions, make a new type of player unit that faces the other way etc, but you can make most of what you need through duplicating the player one stuff and making minor adjustments.
even on one controller you'd want to know which player was which to determine who wins, who the default target for offensive/defensive abilities should be, what side to stand on, etc etc. So that doesn't make things any easier per se but either way it wouldn't be too difficult to implement with some basic GML skills.