After a bit of testing with my friends in game and searching through the wiki I cannot find any reasoning behind how boon removal order works in this game. Duration, intensity, order applied, or even type of boon. None of these factor into what boons are removed when someone uses boon rip. For example, stability is an extremely important boon to pay attention to in all game modes. If a necromancer wanted to corrupt the stability on a guardian and the guardian has four or five boons there is no way the necro can ensure that he will get the guardian's stability with just one well timed skill. This also makes it so that, ironically enough, the best way to counter boon corruption on boon heavy builds is to simply spam more boons so that you have a higher chance of keeping the important ones.
While this seems like just a PvP and WvW issue I feel like it has left a design space unused in PvE. If there was some way to specifically target boons you could theoretically make more precise builds in raids and fractals that only corrupts the boons necessary. This could also lead to more boon usage overall because players would not need to corrupt a full bar of boons to rip protection 100% of the time. They could choose when to rip to get the most value out of the skill. This would also allow Anet to show the value of boons to newer players if they went back and rebalanced older content. Corrupt boon wouldn't seem like such a useless skill in open world then.
For a suggestion on how to design a system I would look at our current condition system. Conditions in this game are cleansed in a last in first out system. This allows for condition builds to try and ensure damaging conditions stay applied through small cleanses by placing less impactful cover conditions on top of it. Why dont boons work the same way? It would force players to think about what order they apply boons in to keep the most important ones safe from small removals. This would allow greater consistency for boon stripping classes as well to know what exactly they are corrupting.
With the next massive balance patch coming up aiming to make the game more consistent and force players to use their cooldowns tactfully removing this unneeded randomness would only reinforce this. Allowing those who pay attention to be rewarded by protecting their boons, and rewarding clever players who can snipe those same boons at the perfect moment instead of simply spamming more corruption and praying.