get latest works recursive (it will impact the chosen item plus everything in it - if it's a folder). So in your case, in the webUI, select the items you do want to getlatest:htdocs/crmkb/webappshtdocs/crmkb/csshtdocs/crmkb/index.aspxand do Get Latest... Simple, no?
I haven't tried this myself, but maybe you can play with using the "private" mode for those files/folders. I know that it prevents a file (not sure whether it can apply to folders) from being submitted, so perhaps it also prevents it from being updated via GetLatest.
How about 'to not allow get latest for this folder'? can we do that?