Steam does that with like all games you install if you don't install the extra junk. You can either install it and it goes away or you keep hitting no each time you install it. It is setup like that because Steam doesn't know which version you have so they make sure when you launch the game you install the correct one that came with the game.
My problem is that I did intstall it. Each time I launch it still prompts me to install it again. Whether I reintall it or not the game launches fine. I'm just getting the annoying message to install msiexec everytime I lauch no matter what I do.