It might be fun to have the Republic cruiser fitted with a bomb so when the Feds find out the investigators are Jedi they think twice about attacking them so Sidious remotely detonates the bomb blowing up the ship making them have to act which would further drive them into joining Dooku's Separatist group as he thinks the Republic is under control of a Sith Lord and the Feds have already been tricked by them.

ESB showed that making deals with Sith Lords usual ends in trouble, it would be cool to see that from the beginning.