It may be a pun. Looking up magma in the French wikipedia*, another name for magma in French is groupoïde de Ore†. Here Ore is a Norwegian mathematician, but ore in English is mineral-bearing rock, whereas magma (in both English and French) is molten rock.
Would Bourbaki have based a mathematical term on this pun? I'm not in a good position to judge; maybe somebody else could comment on this.
* Since Bourbaki was a pen name used by a group of French mathematicians, this is the right language to search in.
† The other name for magma in English is just groupoid. The additional de Ore in French suggests that groupoïde may have had another mathematical meaning in French at the time, which would explain why Bourbaki felt compelled to coin a new name.