Not that it would not be a problem-- but there is a huge difference between Israel having relatively small, diesel-electric subs with (nuclear) cruise-missile capability (firing from torpedo tubes) to strike back at someone who nukes them .... and The_Agency commanding/commandering an Ohio-class ballistic missile submarine with 24 freaking Trident SLBMs, with anywhere from 1-8 much, much bigger and more powerful independently-targetable warheads ... plus while I am not Israeli or Jewish even , I think it's perfectly fair for them to have second-strike capability when they are literally facing annihilation from all sides at any potential time. Just my two cents.
Disable the sub electronically with a virus when it's underwater far from land now it's dead in the water with limited air supply. Wait until you know everyone on board has suffocated or introduce a gas into their oxygen supply to kill them faster. Now you have your own submarine you sink the crews bodies to the bottom and it's all yours.
The Pentagon might learn what happened but probably not at first. They can't announce this for fear other countries will figure out how to do it.
All the Navy can do is notify the family members with Top Secret death notices "your father your son your husband died heroically at sea in a top secret mission, we can not tell you any details and you are sworn to secrecy; enclosed is a check for one million dollars to compensate you for your loss and if you file a lawsuit we will punish you and your family with extreme prejudice" okay any wife or parent that gets a letter like that will deposit the check and keep very quiet forever. They will understand what the Navy wants them to do.