The title says it all.

On my server, players die when hitting water or lava but some jumps are near impossible now.
For example, it is now impossible to jump on a lilypad in the middle of a lake because you'll get killed when landing. Jumping next to water is impossible, being on a block and sneaking above water kills you now.

Instead of setting water as a death block, set DieInLiquid to true in the config.yml.

OnCourse:
    DieInLiquid: true

After some testing, it turns out that it's the ParkourKit death block check that's causing the issue.
It works just fine when using DieInLiquid.

But we were looking forward to turning off DieInLiquid (and to move that to ParkourKits) to create aquatic parkours to use the newest swimming mechanics...

Yeah, it was just meant as a workaround for now. We've already tested a fix for this. It should be downloadable from the Releases tab some time soon.

@steve4744 Fixed this issue and is in the latest (v5.3) release.