The short answer is that the Rule of Two is not absolute1: the Sith can (and often do) utilize non-Sith Dark Jedi (like inquisitors) to accomplish their goals. With an entire galaxy to rule, it's understandable that the Sith would use Dark Jedi to help root out Jedi and rebels.
It is perhaps better to view the Rule of Two as a system in which only one Sith is the Master of the Order, and his apprentice is the heir (and there can only be one heir). But that's not to say the Sith cannot have dark side allies; all Sith are dark side users but not all dark side users are considered Sith.
Moreover, the Rule of Two was created by Bane in part to prevent the Sith Order from weakening itself from within and thus making itself unable to fight a strong Jedi Order. From the Rule of Two novel:
The Sith had existed in one form or another for thousands of years. Throughout their existence they had waged an endless war against the Jedi … and one another. Time and time again the followers of the dark side had been thwarted by their own rivalries and internal power struggles. A common theme resonated across the long history of the Sith Order. Any great leader would inevitably be overthrown by an alliance of his or her followers. Lacking a strong leader the lesser Sith would quickly turn against one another, further weakening the Order.
But with the Jedi Order mostly destroyed by the time of the Galactic Empire, it was less important to maintain the Rule of Two. The Sith still had to guard against internal conflict, but they no longer faced such a significant threat from the Jedi.
Also, Palpatine could not hunt down rebels directly. Part of Palpatine's hold on power depended on his public image as an old man viciously attacked and deformed by the Jedi attempting to seize power. It was not well known that Palpatine was a Sith Lord. The canon novel Tarkin indicates that not even Grand Moff Tarkin knew that Palpatine (and Vader) were Sith -- he only suspected it:
There were many stories about what had occurred that day in the chancellor’s office. The official explanation was that members of the Jedi Order had turned up to arrest Supreme Chancellor Palpatine, and a ferocious duel had ensued. The matter of precisely how the Jedi had been killed or the Emperor’s face deformed had never been settled to everyone’s satisfaction, and so Tarkin had his private thoughts about the Emperor, as well. That he and Vader were kindred spirits suggested that both of them might be Sith.
Palpatine's true genius lay in his political prowess anyway -- he was more effective as a political ruler than a combatant. He did kill a few Jedi in personal combat during the Clone Wars, but he politically engineered the destruction of the entire Jedi Order.
Overall, there were many reasons for the Sith to use Dark Jedi to help them. On the other hand, the risks were fairly small: Palpatine was very powerful -- even Vader was too afraid to confront the Emperor by himself. Palpatine's downfall was ultimately due to his miscalculation of Vader's love for his son, not because he took on dark side allies.
1Palpatine's master, Darth Plagueis, did not obey the Rule of Two absolutely in that he allowed Palpatine to take on Darth Maul as his apprentice. Palpatine himself obviously did not obey it absolutely, either, and Vader took on a secret apprentice. It's not the Rule of Exactly Two.