I'd say that if you really care about having dual installs (one off-steam for mods/leagues, one in-steam for online), you could consider buying a separate key for steam. This would allow you to update both independently... The offline install(s) would still work as it does, and the steam one would open you up to play online with the new contingent of incoming players running the vanilla game. Plus it's not an overly expensive game, and you'd be (even further) supporting a kickass developer.
Me, I don't really do online, so I'll convert to steam and mod the steam install itself. Reiza might even consider adding steamworks mods down the line, too.... That would be great!