It only does this with older Valve games, not other games I might own that are also available via Steam? Say, Civ 4 or X3?
I believe it to only be Valve games, it might even only be Half life and it expansions that it does it to since that's the only Valve games I have. I have Civ 4 and have not had Steam react to it at all like it will if it finds an install of one of it's own.
I've been told by numerous other Steam users that auto-load can be turned off.
My autoload has been turned off since Steam's inception and I've never had it pop back on. Just if you reinstall it you have to turn it off again.