If you want to experiment, try my speedrefactor branch of CuraEngine on github. It does always smooth out extruder speed changes gradually (during the layer, not only on layer change). It works both for the first layer, and for sudden layer time changes.
It helps for some objects. Here is an extreme one: (left: old code, which suddenly slows down, right: speedrefactor branch)
It works well, and I still use this branch myself for printing. But I think I have broken dual-extruder support. Also, it does not help as much as I hoped, so I'm not pusing for upstream integration.
(Note: the XY speed will still jump after the first layer. But it is now calculated such that the E speed does not jump.)