Given she's a gunslinger, Bad Future Applebloom would prove best to use an analog of either a Remington M1867 Rolling Block Rifle, or a Sharps Rifle. Scratch that, given it's evil Twilight, and she'll probably have magical enchantments developed that could withstand gunfire, I'll go straight for a Nitro-Express elephant rifle. If Bad Future Applebloom knows unicorns who does magic, they can enchant the ammunition for extra penetration and even explosive capabilities.
If you want to wipe out a group of these bastards, imagine if you will, a town, an area full of mesas, or a woodland. Designate an area as a kill zone, and position your gang of sharpshooters with wild-west sniper rifles around said zone at a range of a few hundred meters, hidden in camouflage so that the tyrant's pegasi royal knights can't see them from the air or on the ground when they scout. Have some sort of bait in the zone's center, say an old campfire with sleeping mattresses around it, like an old campsite built by rebels, to lure and converge them into the kill zone to investigate. When enough of them land and fold their wings, open fire.
Assuming a standard Royal Knights squad has around ten soldiers (From the Bad Future Royal Knights picture by Astringe), if all of the sharpshooter ponies aim accurately, firing simultaneously, you can take out half of the soldiers before they realize what's going on. Aim for the commander first - decapitate their strongest and smartest soldier to sow disorganization within their ranks. Given they're wild west rifles, there might be a delay (I think) in reloading. If there isn't time to reload, drop the sniper rifles and blaze away with repeaters. Firing from all sides, the royal knights would be minced. If it isn't too expensive, mine the kill zone with explosives, detonate by a TNT detonator.
As a matter of fact, why even take them in the open? According to Astringe's Bad Future lore, the Royal Knights are enhanced by dark magic. Engaging them in the open would be dangerous given their speed in the air and strength. Luring them into a dark, enclosed area where they cannot fly or fight properly would take away any advantage they have. I suggest another rock mesa, or mine shafts with narrow, snaking tunnels; both areas have plenty of room to set up ambushes and be rigged with booby traps (Don't even need to be explosives; pit traps with sharpened sticks, for example). Close off the exits the moment they waltz in, and as long as you don't fight them head on, engaging in ambushes and sharpshooting, the knights would be decimated.
Bad Future Applebloom should be ruthless and practical when dealing with the Royal Knights. These guys are monsters, as the description and lore goes, soldiers who abandon their equinity to embrace dark powers and obediently commit atrocities for their tyrant. They are rabid attack dogs; and those kind of dogs... get put down.
Of course, some people would disagree, saying such dishonorable tactics would make the guile heroes no better than the enemy they fight.
Well, there's war crimes, and then there's being guile. In a revolutionary war against tyranny, the ruling tyrant would always have the advantage in units and resources that could be deployed, and amoral ruthlessness to accomplish their objectives wherever effective. A true tyranny will have no legal or moral hesitation to use whatever means necessary to crush opposition and maintain an iron grip on power. And for their own interest, they'll do whatever it takes to hide it to in order to demonize the opposition.
A resistance movement fighting a guerrilla war against the tyrannical authority must use every single advantage they can get if they are to fight the forces of the dictatorship. There's no way around it; freedom and victory demands sacrifices, whether in blood, or in one's conscience.
It's not the same as asking Bad Future Applebloom here to break every rule of war and commit atrocities whenever she goes if she ever decides to go up against Bad Future Twilight's dictatorship. Circumstances however would inevitably mean she must at least bend the rules, if not use any means necessary, if there's any hope for her and her friends to win and liberate Equestria, especially against an adversary as capable, and presumably as ruthlessly efficient, as Bad Future Twilight.
Now the question is, does Bad Future Applebloom have the courage, moral or otherwise, to do what is necessary?