Williams are just trying to be awkward. Okay, they don't agree with everything FOTA has to say, but their actions seem a little bit petty to me.
I think it's a little misleading to say FOTA would be annoyed. I suspect a few teams would be annoyed and others would not. McLaren, for instance, have been making noises for quite some time about using KERS next season, but Toyota (the usual hardliners) want to see the back of it. More likely, a row could erupt within FOTA, which would satisfy Williams' childish agenda and give power back to Ecclestone and the FIA.

Ayrton Senna: WDC 1988,
1989, 1990, 1991
McLaren: WCC 1974, 1984, 1985, 1988, 1989, 1990, 1991, 1998,
1999, 2007McLaren: WDC 1974, 1976, 1984, 1985, 1986, 1988, 1989, 1990, 1991, 1998, 1999, 2008