Wouldnt any changes you make just be saved as a .esp file? Then you can uncheck it whenever you want... At least, thats how it was in the past ES games.
(just realized i was in the CK forums..)
It depends (I think ...) what script/fragment you are planning to alter. And (maybe ...) how you alter it (inside CK or external). The script files are in their own directory under the DATA folder, so if you amend those directly (outside of CK), any changes are permanent for all MODS you release (unless you do the backup fudge). I am not so clear on what is amended when you edit inside the CK.
So, while changes are saved to an ESP (and or ESM) it is possible (likely ...) that it may also amend the vanilla files
Best practice is to do your very best to amend/change/remove as little as possible from Vanilla, and find a way to make your own stuff which impacts on Vanilla items. Usually, there is a way to do what you want, without editting Vanilla (but not always ...)
Note: There is also the issue of you amending Vanilla Script A and another modder amending the same script ... That will/may cause lots of incompatibility problems (for both of you)