As a temporary work-around, if you put the hashtags at the end of another paragraph (not at the beginning of a new line) then Markdown will leave them alone.
I’ve actually been thinking lately about adjusting how we handle hashtags. As everyone knows, Micro.blog doesn’t actually support hashtags. But now that we have Mastodon posts flowing in with hashtags, we may want to do something to make them look more consistent, even if we still don’t link them to search.