Shrine of order = lunar?

[beanboy]

Can this ruin my commando challenge for the new ability?

[Spoopy]

It's not a lunar item, so it's fine. However, it can easily ruin your run in many other ways so I'd still not do it.

[JHarlequin]

The shrine of order counts all your items of each particular rarity and chooses one of them of each rarity and gives you specifically that many of that item.

So if you have five goat hoof, five syringe, four extra clip, and three leeching seeds, two guillotine, one fuel cell, and an aegis.

That would be 14 common items, six uncommon items and one legendary. You could end up with 14 goat hoof, six guillotine and one aegis. So you lose all the other items and only have one stack of common, one stack of uncommon, and one stack of legendary.

It never changes rarity and Lunar is it's own rarity, so if you don't have lunar items, you can't end up with lunar items.

As for the deal of picking up a lunar item, it is picking up the item, not spending the lunar coin that matters. You could go to the bazaar and buy each of the items but as long as you don't pick them up your commando "uncorrupted" run would be fine.