How can I remove unwanted line breaks in imported text without having to do it line by line manually?
What kind of text documents do you use? One possibility might be WordService (see our downloads page), another one AppleScript.
Are you aware of BBEdit (previously TextWrangler) to re-structure text? Would this be what you need?
Brett Terspstra put together a large collection of Services for working with Markdown, one of which does what you want. See http://brettterpstra.com/projects/markdown-service-tools/. They are free to use. Brett’s site is well worth visiting for all sorts of reasons.