You can control which packages are loaded through the variable package-load-list. Set it in your init file, before calling package-initialize if you do this explicitly. You can reach it from the Customize interface (“Package” → “Package Load List”).
package-load-list is an list whose elements are lists whose first element is a package name (as a symbol). The second element of the list can be a string to force a specific version of the package to be loaded, t to load the latest version (the default), or nil to disable the loading of the package. Also put all in the list, so that Emacs will load the latest version of packages which are not explicitly mentioned.
(setq package-load-list '(all (unwanted-package nil) ))