Fafner in the Azure (2004), most probably.
The story is that of an island fighting against the Festum, yellow crystalline monsters. The Festum have an "assimilation" process, by which the target gets crystallized, shattered and incorporated to their hive mind (the Mir).
The Fafner (the big mecha humans use to fight Festum) weaponize Mir components, but the more they're used, the more the Mecha pilot risks getting crystallized themselves. For instance, this woman (S01E23, "Decoy"):
As for the "monster being a kid", Wikipedia has this bit:
Many of them are killed by the Festum in a process of assimilation. In desperation, they order the deployment of a mecha called the Fafner Mark Elf, but its pilot is killed en route to the hangar. Left with no further options, they send a young boy named Kazuki Makabe as the replacement pilot assisted by Sōshi Minashiro from within the Siegfried System.
I found it by memory, having previously identified that anime for Anime in which people in mecha suits fight yellow monsters, but the more they fight, the more they turn into crystals and eventually die.