If a question is asking for support of a thesis, should answers that contradict the thesis be given? Those anwers are often found in comment which is not really supposed to be the right place.
I don't have a strong opinion on this generally - honestly the key thing about answers is for them to be helpful and well-researched. If you feel that you are able to contribute in a way that genuinely helps the person asking the question, then I'd encourage doing so, even if it doesn't comply to all assumptions they have asked answerers to make.
After all, we do have a good voting system here on BH.SE - the worst that can usually happen is to be voted down. I'd hope that genuine and courteous answers - not just contradicting over petty theological differences - would be received well by most within the community.
On the other hand, often users do ask these types of questions where they're explicitly seeking to explore or test one side of an interpretive issue. So the most helpful thing to do is often to 'lean in' to the assumption and begin from there. For example you may try your best to reconcile the assumption with the text, but honestly admit/critique where it falls short or generates apparent contradictions.
However, I do agree with you wholeheartedly that the Comments are the wrong place for such answers. As moderators we do often end up deleting waste comments like this where users are leaving petty throwaway grumblings about the assumptions themselves.
It's okay to comment with questions or clarifications around any assumptions, especially as it can help Answerers to understand exactly why that assumption should be made. Insulting the asker for any reason - even subtly - should be wholly avoided.