Well, as you can see, the vibrato settings are part of the sample view, because that's how it works in IT. Just because you edit an XM, this fact doesn't change anything internally, and in fact, if you were to re-save your XM file, OpenMPT would have to write out instruments again anyway.
In your specific case, you could simply use OpenMPT itself to convert the file to MOD, which would get rid of the instruments and auto-vibrato anyway. OpenMPT does a pretty god job and mod conversion anyway.