Every class - alongside Sentry Guns - can prevent Super Scouts from progressing by simply standing in their path. While this can work for every class - this strategy usually is only recommended for Sentry Guns and Heavy, as other classes generally lack the bulk to survive, and unlike Sentries or Heavy, take more knockback than the two.

If you do plan on Body Blocking - it's best to stand around corners, as Super Scouts tend to take turns tightly.

In the event a Super Scout gets behind, you need to get to them as soon as possible, as they will deliver the bomb rapidly. Any tool & upgrade that makes you faster is critical to handle Super Scouts, as they otherwise will get back to your base before you can react.

While I do not recommend running this Canteen under normal circumstances - as you're losing out on DPS with the Crit Canteens, survivability of the Uber Canteens, and the longevity of Ammo Canteens - this can be a life saver as a last resort option to deal with Super Scouts.

It should be noted that alongside returning to spawn, it will give a 5 Second Speedboost upon activation, giving you a little extra speed to catchup before the bots arrive.

Mad Milk is already considered Scout's defacto best option in Mann vs Machine, but on top of just being really good for tanking damage - it also comes with a Slowdown Upgrade.

For 200 Credits, you can purchase the -35% Speed On Target Upgrade - which will cause all robots to be greatly slowed for the entire duration of the Mad Milk.
With one throw, you can stop every Super in the game

While less common than the Fan o' War, once you can comfortably afford the Ball Marks Target Upgrade, it practically becomes a replacement for the Fan o' War.

But alongside just being good for marking Robots, the ball by default can slowdown robots at far enough distances.
On paper, this would be really good - but in practice comes with a weird bug.

For whatever reason, if a Robot becomes Ubercharged - for instance, getting chipped at while leaving their spawn - the Robot is immune to the Sandman's Ball, and thus immune to its slowdown effect.
Due to this inconsistently, while it can be a decent option to deal with Super Scouts, you're better off just using Mad Milk to deal with them.

But outside of that, the Sandman is a good weapon in general, just not optimized for dealing with Super Scouts. Note that the Mark for Death effect also applies on hit with the Bat Itself.

You might be tempted to try stopping Super Scouts using the FaN's Knockback to launch them into a pit, but simply put, it's not effective for that purpose

If anything, you're making it harder to shoot the Super Scout for the rest of your team - while the knockback fails to push the Scout for more than a few seconds.

A singular tick of Rocket Specialist is practically required when playing Soldier effectively.
On top of having a faster projectile & greater splash radius, it also comes with a slowdown effect on it.

While not as long lasting as Jarate or Mad Milk, mixed with a fast firing & reload speed, it can still be an effective way to deal with Super Scouts.

But in the event you're in the earlygame, there may be a better option to deal with Super Scouts.cx

More often than not, you've likely seen (or even have been) a Pyro that knocks robots into environmentals.
It's a viable strategy - but due to the map & position sensitive nature of this strategy, it's rare to benefit from it without abusing Airblast.
PSA - Don't be that Pyro that tries to force airblast kills.

I've seen this strategy exclusively on Ghost Town by one or two Pyros.
If you max out the Reload & Firing Speed of the Scorch Shot, the knockback can in theory prevent bots from progressing.

But similarly to Airblast Spam, it's a bit rude to do so over & over again depending on who your team ins playing as.

While you rarely see Heavies running this Minigun in MvM, it's possibly the single most effective way to deal with Super Scouts in the mode.
As every Bullet will eventually lead to a Robot being slowed to the speed of Heavy himself, you can effectively make all Super Scouts stop, giving your team plenty of time to wail on them to death.

Main catch - you're giving up 25% of your damage to do so.
But if that tradeoff is worth the cost - or otherwise is a necessity to progress - go use it, it's actually really good for its niche.

If you're unable to run the Natascha for whatever reason, this upgrade can on paper act as a substitute for slowdown - instead pushing robots back.
But in practice, this is a 350 Credit Investment for basically just this purpose.

Due to the ability temporarily halving damage, it's impractical to use it for anything more than stopping robots from deploying the bomb, or pushing them into a pit or earlier section of a map.

Similar to Scout's Mad Milk, Sniper's Jarate has his own Slowdown Upgrade for the same price as Scout's.

However, due to Jarate having more competition in the Secondary Slot (mainly due to the options of the Cozy Camper & Cleaner's Carbine), it's harder to run Jarate when there's more consideration to that slot. But when you do run Jarate, it's definitely worth it to stop Supers, alongside marking robots for death.

While the upgrade is really good for almost everything - and still is Sniper's Best Upgrade - it's slowdown is not the most practical option in terms of dealing with Super Scouts.

Due to the strange nature of Giant Hitboxes, and with how rapidly they're going to be moving, it's almost impractical to land a headshot against them, let alone trying to repetitively land headshot after headshot to keep them slowed for long periods of time.

However, it should be noted that the resulting Explosive Headshot's radius does slow anyone in its radius - so you may be able to slow a Super Scout by targetting another robot first.

Without even upgrading the Sapper - it will entirely Stun small robots, and Slow any giants impacted by it.
For just being part of Spy's default kit, it's a great way to deal with Giant Scouts.

Only problem is you have to actually play Spy for it to work.
(and also the only non-time way to recharge it is using Ammo Canteens)