You will indeed, Cyber-Slig, and even then I don't think you need to kill every single one. But to avoid the tragedy of having to go through the whole game again, make sure you're relatively meticulous with what you kill: drop egg crates on each other, chuck Natives off cliffs: go nuts. Just remember you need to get some Muds through levels alive to open doors before you wipe them out.
And SS, I don't think that's exactly true. Using the Path Skip would prevent you from rescuing any Mudokon you skip past, but places like Necrum where there are no Muds for long periods of time, you can probably skip past - like past all those annoying Fleech levels.
