My github pages repo is based on https://github.com/maciakl/Sample-Jekyll-Site. To achieve this I cloned https://github.com/maciakl/Sample-Jekyll-Site then manually changed the origin in git config. But now my repo has all https://github.com/maciakl/Sample-Jekyll-Site's commits in its history. Is there a way I can get rid of them?
Clone with depth 1. This will get you the current state of the repo, without any history.
However, it is questionable if this is really what you should do - in general, the commit history contains a lot of valuable information.