Shugdenlibrary,
I see the point you're making, but I don't agree with your conclusion.
Firstly, this Holy shrine set up was overseen by H.E.Tsem Rinpoche.
Secondly, it looks to me like the shrine is saying 'Dorje Shugden protects all of this', not that he is 'greater' than anyone.
Thirdly, by your logic, we may as well include the fact that Buddha Shakyamuni is towering over the Guru. According to the Lamrim, the Guru is more precious than even Buddha Shakyamuni because he cares for us directly. Also, you may as well complain about all the lineage Gurus towering over Buddha as well as the Principal Guru of the Kechara mandala.
Fourthly, keeping the refuge commitment to regard every image of a Buddha as an actual Buddha, I prostrate to this assembly of living Holy beings who are none other than my Guru. May Shugdenlibrary be blessed with rapturous delight and humility in your presence!