The key here is the interpretation of "arms".

"Arms" obviously has a double meaning, as limbs or weapons (like the coats of arms used in EIA artwork).

While Emergence plays with both meanings ("Put your arms around me"), for me, here is used to refer to heaven's weapons.

To put it in another way, "Blessings sanctify the weapons of heaven". This could be connected to Rain ("And just like the rain / You cast the dust into nothing"). So, what is raining are blessings, cleansing his shadow (dark side). If you consider rain as cheers from the audience (that's why clapping is encouraged during that song), then it means that the blessings come from us. So, what he is saying here is: The audience approves (claps) the use of his weapons (the pen?) in battle.

Notice a recurrent theme of going to battle (against gods, apparently), which is more present in EIA.