This is sort of a continuation of an earlier question I posted.
In Revenge of the Sith we see how General Grievous' ship is attacked by clone troopers even though Palpatine, Anakin and Obi-Wan are aboard it. Why would they do that? The forces of the Republic knew for sure that Palpatine was there as they sent Anakin and Obi-Wan to free him, and consequently they could also expect those two to be aboard.
Why would they take the risk of killing the Chancellor and two Jedi? Did General Grievous' ship pose such a threat?