I'm using Mysend.py to post messages to Movable Type from the command line. I had to hack up the rpc-xml code within MTOS, but its still worth it.
This is the default template header I'm using:
title: CATEGORY: CONVERT BREAKS: markdown_with_smartypants
Hopefully it supports the tags option.
UPDATE: It didn't support the TAGS option right out of the box, but with a quick change its now supported. I added this around line 721:
elif key == 'TAGS':
post['mt_tags'] = val