It's an interesting question. In the original X-Com the Accuracy of a soldier is reduced if they are not at full HP (this happens during battle too), and I've been wondering recently whether to put that system in the game.
Specifically, they reduce Accuracy by 0.25% for each % of health lost. So if you're on 60% health, your Accuracy is reduced by 10%. Not actually a huge penalty but it's still something.
The reason why I think it might be a good idea is that it solves the problem you've mentioned here, but also solves another problem - whether reaction fire / overwatch is worthwhile against tough enemies. Basically in a lot of cases reaction fire just isn't worthwhile if it doesn't immediately kill the enemy, because an injured enemy is just as effective at attacking you than one on full health. If we use the X-Com system then hitting the enemy with an overwatch shot would reduce their Accuracy and make them less of a threat, even if they're not actually killed.
What does everyone else think?