Well really it all depends on you, not the boat... depending on your skills you will be fine, or you will die, or you will have an experience somewhere in between.
Do you have a really good roll and self rescue skills? Are you going alone or with a great crew. Do you have much/any whitewater experience? Have you been down the EFC at lower flows or are you planning to take a sea kayak down at these relatively high flows (~3,000cfs) that are occuring now. There is no simple answer to your question, but in general, the EFC is not a place to take a non-whitewater boat unless you are an extreme expert in the sea kayak (i.e., you like to play in the surf zone around breakers & rocks and are very comfortable rolling).
Have you taken your sea kayak down a relatively easy whitewater run such as C2G on the SFA? If not, you are going to be in for a rude surprise and will probably lose some/all of your gear as the EFC flows fast and cold with lots of very strong eddy lines and boils.
IMHO, if you have to ask if it will be "ok" to take an inappropriate boat down a class II/III river during peak/cold flows, the answer is, no, but it's up to you in the end.