There's always option to convince her to just drop this whole war business and move elsewhere, avoiding the fight altogether...
If you do insist on fighting, the queen has pretty hefty resistance to kinetic damage; the flare gun you can pick up in the factory basement can work around that nicely. Saving the tranquilizer so you can use it on her and soften her up also makes things easier. As does sabotaging the tank beforehand, so she cannot use it. And in the end, brute forcing it by simply chucking grenades at the problem can work surprisingly well (since it takes out other targets while damaging the queen, providing some breathing room for your allies)