If your map can be beaten in 30 seconds when it's supposed to take 2 minutes on-track, your map is poorly designed. Harsh truth. It's not cheating; it's just a consequence of this bad design.

The real problem is that your map is poorly laid out, which allows people to make those gigantic skips in the first place. Blocking skips is just a bandaid solution that doesn't actually fix your map, will just make speedrunners want to skip your map even more to prove you can't stop them, and goes directly against the game's core concept that the roads are just a guide, and deviating from them to obtain a faster time is perfectly acceptable. Trying to block skips using direct means like killgrids is about equivalent to trying to fix a broken building with sellotape.

Disabling abilities isn't a good method of skip preventation either, since it can takes away both the freeroam and jump/boost/roation mechanics, and just makes the game less fun. As well as the fact that skips are still possible without those abilities - it's just an artificial limiter.

What you should really be doing to stop ridiculous skips is laying out your map so they can't be done in the first place - if it can be done, it will be done, so avoid mistakes such as placing the end zone too close to the start, or having track that loops over itself a lot (what we call "spaghetti track"). Lay out your roads in a linear fashion to avoid this, especially make sure the start and end zones are far away from each other.

Other methods include decorating the skip routes - this makes them shortcuts, so they aren't skips anymore - or you could place a hidden teleporter that's faster than the skip, similar to the one in the official map Corruption.

Remember that you're the map author, and therefore have the ability to discover skips to prevent them before anybody can use them; use the power of foresight to notice potential cuts and stop them before it's too late.

But one of the biggest sins you can do when it comes to skips is blocking skips after people find them. That's essentially a federal crime in the Distance community, as it leads to times that are impossible to beat with no way to remove them without resubmitting the map or asking Refract themselves, as you just found out - and it also goes against one of the game's core mechanics, as I explained previously. Just don't do it.

If someone finds a skip you didn't want, you can either use the shortcutification or hidden teleporter methods I mentioned above, or just leave it as it is - after all, for better or for worse, finding skips is an intentional part of the game, and you will never be able to stop them unless your map is a nearly completely straight line - and even then some people may be able to find some unintended faster paths through it. Stopping skips is impossible, and you have to learn to work with this fact, like it or not.