One of the issues I could see with this is that technically this isn't self inflicted harm. This is a mechanical choice that the player makes, but the character will often take this damage from outside sources. Consider if I'm in a gunfight and I fail to break a block of cover fire on my attack. I take the consequence "Grazed" to make my roll. Technically the character was wounded by hostile gunfire, not by himself.
It's really a thematic issue though, I think the mechanics work ok.
A character with Recovery or Toughness Powers may, in actuality, not be subject to certain types of Blocks owing to their powers. A Guns-based Block on a character with Full Immunity, for instance, just doesn't make any sense. There may be a sidebar comment addressing this, but I can't remember where it would be. Probably under the mundane Block rules.
Edit: I failed to find it in the Block rules.
But the main issue with self-inflicted Consequences seemed (to me) to be in the fields of Evocation and Thaumaturgy. If it's a normal gunfight, I'm not that bothered by a Recovery monster letting itself get chewed up to make a few rolls. In magic, though, using your Recovery-blessed teammates as mana sources seems more problematic.