Executive producer Warren Littlefield revealed enough to assume there will be questions or repercussions for what happened, and with higher-ups sniffing around at the commander’s household, they may catch wise that he hasn’t operated like the typical Gilead commander for a while now.
One would imagine that if Commander Lawrence has been wrapped up in the resistance prior to this, he’ll have to lay low given Emily’s attack on Aunt Lydia in his house.
With Emily gone, its possible he could craft a scenario that leaves him free from blame in regards to Lydia’s injuries, but that would seem to depend on how much Lydia remembers from the attack.