Not directly. I didn’t think it through but you probably could get what you want with some AppleScript by
The step of creating RTF files is not necessary, I think, but you probably first want to check whether the conversion’s result is what you’re looking for. If it’s ok then it should be possible to convert and add to OmniFocus without creating files.
Here’s a demo script. Use it to test whether
pandoc's conversion would suit your needs (links are converted, but I’m not sure if everything else gets converted). Set the paths and try it in
set theOutputFolderPath to (POSIX path of (path to desktop)) as string
set theInputPath to "/Users/USER/Markdown.md"
set theOutputPath to theOutputFolderPath & "Test.rtf"
set theShellScript to "/usr/local/bin/pandoc -s " & quoted form of theInputPath & " -o " & quoted form of theOutputPath
do shell script theShellScript