Harry may not be in the best PR position right now, but he's a wizard of Noble House and great renown. Killing Harry would work much, much more poorly for Lucius than killing a Mudblood that everyone believes escaped Azkaban on technicalities and dirty tricks. And, y'know... their whole thing would appear to outsiders to be an elementary-school romance, so it's not unreasonable for someone in Lucius' position to assume that Harry will get over it before he's in a position of causing any serious damage.