My main issue is with starting under safety car. If they're physically leading the cars around the circuit, then there's no reason the race can't start normally and let the drivers pick their pace (indeed, Button complained about starting Malaysia 09 behind the safety car as it created even more spray). Stopping the race at Canada this year was different - if the track is that waterlogged that you have to physically stop a race, then it's too bad to start under safety car too.
Basically, if it's too waterlogged, red flag. If it's not so wet the cars can't be led around, then they should race.
But sometimes it takes a few laps of the field of cars to clear away the spray. Under race conditions this can be dangerous. Behind the safety car it is less so, as the drivers aren't pushing. The only problem here is it makes the restart dangerous with low tyres temperatures etc. But I think that was compensated for in Canada this year as it was nearing the conditions required for inters, meaning the full wets would have come up to temperature very quickly (Though the same can't be said for the brakes).