@narcio - yes what you are doing is the only way. I did raise this exact issue on the development thread for this plugin.
My further thought on this was that the problem you are trying to solve now is a merge issue. As what you are wanting to do is merge those book rows together, taking into account that for any binary duplicate formats within that set there is no user intervention required. My idea for a solution for this which I also mentioned on that thread is a new "smart merge" plugin. This would just be another type of merge, but give you a popup dialog detailing the books and formats in the selected rows. So you could double click on formats that are duplicates to view them to decide individually which to keep etc. If there are no duplicate formats within the group, or if the only duplicate formats are binary duplicates, then it will be able to make all the right decisions for you without you rolling up and down the rows trying to figure out which duplicate formats there are, opening them up and trying to remember which format you opened from which row etc.
However that is nothing more than an idea for a plugin at this point, and it has had no serious thought on what it should look like. There is also the question of book metadata, as to whether as a user you should be able to pick and choose fields from that to win. Thinking about this now I think that is unnecessary, particularly given how much better the metadata sourcing is now in 0.8 compared to previous. It could always be added as a later feature with a second tab anyways if it was thought worthwhile.
So the only other problem is the viewing of formats. In a perfect world what I would like to have is a side by side ebook viewer for this scenario. So you could pick a format with duplicates and open up that format to see them next to each other and decide which to keep. However this is unlikely to ever happen, as it would require calibre changes that would only be useful in this one scenario, and still only marginally so, way too much work.
What might be more practical is if there was a command line argument added to the ebook viewer allowing passing of a window title rather than it just being read from the book metadata. So when you opened a pair of duplicate formats, it would pop open the two book format windows but you could see something in the window title to know which is which from the merge dialog. Maybe this ability exists already, I haven't checked.
Sorry to have rambled onto another subject but my point is there isn't a practical alternative I can think of. What the binary duplicate check is telling you is that you have a group of two or more books that need merging because at least one of their formats is a binary duplicate. A menu item to remove all but one of the binary duplicate formats from that group would be a simpler solution but it only addresses one of the issues that you will need to face when merging the group. I would rather we figure out a more generally useful merge plugin approach that has binary comparison as one of it's weapons to help give a more intelligent merge default.