That is why the thing in your head is for. Cleaning a mod does also mean using your brain. And, yes, I removed those, of course.
At one point though, you have to ask yourself if fixing a mod is really worth the hassle. Especially if, like in this case, the whole thing needs a lot more than cleaning. Cleaning refers to the removal of dirty records, not outright fixing tons of bugs like the messed up activators, the land dreugh, the doors, the faction, the messed up SI scripts, or one of the other bulk of issues.
If you want to do it, then yes, that's fine. Releases in such a state should never ever be promoted or excused though, because I am quite sure that a lot of non-modders (and merely mod users) lack the skills to fix these kinds of problems. It's by far not as simple as running a "Remove identical to master" and "Decompile all" once :rolleyes:.