You can use the IPython API to change shortcuts.
If you use the command IPython.keyboard_manager.edit_shortcuts.add_shortcut, you can change the ctrl-enter key combination so as not to change the focus.
%%javascript
IPython.keyboard_manager.edit_shortcuts.add_shortcut('ctrl-enter', {
help : "run cell and keep focus",
handler : function (event) {
IPython.notebook.execute_cell();
IPython.notebook.edit_mode();
return false;
}}
);
edit_shortcuts command_shortcuts, .
, add_shortcut remove_shortcut, .