I think you are overestimating typical Jedis' capabilities. Anakin and Luke were excellent pilots, but even somebody like Obi Wan was only able to escape Jango's Slave One by pretending to have been destroyed by a missile. Again, at the beginning of Episode III, Anakin was able to evade missiles targeting him, but Obi Wan was not and was only saved by Anakin's intervention.The pilot is a jedi. They can evade any turbolaser fire.
The US navy doesn't have to fight jedi.
It's a small capital ship on prisoner transport duty. It is not "massive", it is not heavily armed and it does not carry marines. And Star Wars has frequently shown Force users ploughing through dozens of hostiles. "numerical advantage" counts for nothing.
And during order 66 we saw several rank and file Jedis been killed by just a bunch of clone troopers. Granted, they were taken by surprise, but Yoda was able to feel the troopers treachery and escape, which reinforces that the main Jedi characters we see in the movies are a cut above the rest.
The two bad guys needed to get on the ship so the plot could happen, but a more competent New Republic captain would have clearly established these two were a cut above the typical Jedi.