After a sincere repentance from committing fornication with one's sister, is looking at her or being alone with her considered a sin that necessitates punishment? And is that considered condoning disobedience and an act of disbelief, especially if it was to avoid scandal or happened unintentionally? Does the same ruling apply to the sister if she does not treat the questioner as a stranger, despite feeling suspicious?

Your question does not involve condoning a sin, and apostasy is not a trivial matter. Your treatment of your sister as a stranger (regarding the hijab and avoidance of private seclusion) is only necessary if there is suspicion and fear of temptation; otherwise, the default is that she is one of your mahram. If suspicion is dispelled and the satanic thought is repelled, it will not harm you. You are suffering from waswas (obsessive whispers), so we advise you to ignore them, seek refuge in Allah, engage in dhikr (remembrance of Allah), seek forgiveness, and perform legal ruqyah.