One way to deal with this, at least in part, is to educate the new players. I'm sure the developers will be providing instructions and guides for the final release. Many who are not enthusiasts of this period of naval warfare are likely not aware of sail spilling as a way to adjust speed. Without that knowledge, it would seem that raising and lowering sails is the way to do it. As well, some players, when armed with the knowledge that there was not time to raise and lower sails during naval warfare and sail spilling was the method used, will also turn to that method in order to stay as realistic as possible.
Of course, there will ALWAYS be some who try to take the easiest way out and they will resort to sail spamming and any other method, no matter how annoying or historically inaccurate, in order to succeed in their own eyes.