Deconstructions are awesome. They don't all mean "smurf you" to the target genre. It's just a post-modern trope used to take certain aspects we have come to understand as obvious apart and showcase some of its weaknesses, how it can be done differently, etc. Basically, it's a play on expectations and how they are valid (or invalid) in a more realistic situation.

That said, Xenogears doesn't really carry many deconstructive elements, to me. Although wait, there is at least one. Ramsus. He kind of deconstructs the typical Dragon Ascendant/Rival/Big Bad of the PSX era. He's kind of built up as this Sephiroth-type character throughout the game, having a link to the main character, as well as a personal vendetta. In the end, he gets offed quite unceremoniously. We see how small he is, how unimportant in the grand scheme of things. In that, I think he might be a deconstruction of that kind of character.