I don't chibi-fied my characters as they're already cartoonish enough. However i simplify their outlines and exaggerate the face when there's a moment to do comedic poses. I use it sparsely and only in small panels.

For your questions, I personally think giving main characters chibi-tized version (in-comic, half-way down the story) is NOT a good idea, especially if your story is a serious one. Good on you holding that decision knowing it could be jarring. Do you have comic relief side/minor characters, maybe they can do it? (just my 2 cents)
If you know this, a serious story such as Berserk (manga) wants to lighten up by introducing Puck the fairy, who is always be chibi-tized for comedy however the brooding protagonist Gut never does. That would break his character and sorta cheapen the seriousness of the story.
Off-comic chibitization of your characters however is perfectly fine, don't worry!
I think you can pull this off eventually. It's really up to you. 