If this was post-ToP Freeza, it'd be more difficult to decide when defending the universe usually gives someone a free pass as seen with Vegeta in the Boo Arc. Since it isn't that Freeza though, I'd argue firmly that Broly is the lesser evil.
Firstly, we must take into account mental stability. When Broly ravaged the Southern Quadrant, he was in a somewhat berserk state as we can deduce from how he acted in his SSJ form when fighting both Goku and Vegeta as well as flashbacks. Yes, his LSSJ self seems to be quite sadistic and of free thought, though that's a different case and his confirmed kill count in that state only numbers several people at best. This counts double for his M10 self who seemed to have completely lost his sanity. Meanwhile, Freeza's numerous genocides and enslavement of entire races were premeditated and entirely of his own will.
On the subject of death tolls, Freeza has a far greater known kill count. Yes, Broly destroyed a large portion of a galaxy, but we have no idea on how much of it had inhabited planets with sentient life. On the other hand, we have a firm understanding that Freeza's death toll through both first-hand actions and his orders is at least in the thousands based on Toriyama stating the Saiyan population peaked at around 1,000 or so, at least 107 Namekians and an unknown yet significant amount of other races from the Freeza Force having actively disposed of planetary inhabitants for over 20 years. Furthermore, the severity of some of the individual lives Freeza took is worth noting, with him having personally killed Earth's former God (Piccolo).