If you don't have elements mapped on them, you can exclude them from the schema in the catalog explorer: select them all in one go (shift/ctrl-drag) then right click and select 'exclude from catalog'. This will remove them from the project. Next time you refresh the catalog, they're not pre-checked, so you can then just check the table you want to add.
Would that work? If not, please let us know why, so we can think of something else.
In v5.6 we've implemented a filtering / search in this UI as well to narrow down the list so you can easily select them in the UI, but other than that, the main design is based on: if you won't map an element onto a table, just remove it from the catalog in the project.