That pretty much answers why we're no longer participating in these.
In my view you can be proud that you cleared those bosses first. You just didn't achieve a full instance clear.
We will never know if everyone had skipped would they have downed the bosses before or after the time you downed them which is why it is hard to validate.
For me all I care about is who completes it all first. (I don't really hold the title in that high regard). That's just because I personally enjoy the initial progression over the finesse of the 2hr kills.
I suggest for the next one come back fighting and prove to everyone what you know your guild can do. The competition will be all the better for having another top guild in the mix.