i'm not sure if it is a bug, because i don't know what destroy should do exactly. Assuming that it should remove the pagination completely it fails for my environment (FF 49.0.2. Win 7).
using the destroy option, all values are destroyed by invoking removeData(). in fact, the pagination well is still shown and even clickable (page 2 p.e.), but throwing an error "s is undefined". i'm not sure what removeData() should do, but it seems, that only the variables and objects in memory are destroyed and the source code still remains. the solution for this problem, which worked for me, was to add following lines to the bs_pagination.js:
line 435: elem.empty(); //to empty the concerning div-container
line 436: elem.removeAttr('class'); //to remove the class-attribute of the div container, otherwise an empty well would be shown