This is what I think is going to happen: Jimmy went way out of line, but he's now already punished for it. After what happened Jimmy will probably realise he's not up to it, as far as he wasn't already aware of that. Nucky will probably offer Jimmy help or Jimmy is going to ask help from Nucky. He will probably step aside so that Nucky could get back on top (which was Nucky's strategy after all based on Rothstein's advise).

When Nucky went to Jimmy and the Commodore to say he was going to step down, you saw that Jimmy and Nucky still liked each other no matter of the situation. So I think Nucky will forgive him and they will make peace. I think the Jew is going to be killed in the last episode.

I could be completely wrong and I won't be suprised to say the least, just a humble speculation. It could very well be Jimmy who is going to be killed in the last episode, but I think his character is too important to kill off, contrary to that guy who plays the Jewish butcher.