Killing the Jedi was already a priority for other reasons: They were powerful in their own right (hence the need for millions of troops), and to get revenge for almost wiping out the Sith. They would always be a threat, regardless of whether Anakin had children.
"Having exterminated through treachery and deception the Jedi Knights, guardians of justice in the galaxy, the Imperial governors and bureaucrats prepared to institute a reign of terror among the disheartened worlds of the galaxy. Many used the imperial forces and the name of the increasingly isolated Emperor to further their own personal ambitions" - ANH novelization
The fact that Obi-wan and Yoda are still alive by the OT doesn't mean the Empire stopped looking for them.
"Kenobi resumed his pacing. "Vader used the training I gave him and the force within him for evil, to help the later corrupt Emperors. With the Jedi knights disbanded, disorganized, or dead, there were few to oppose Vader. Today they are all but extinct." - ANH novelization
The fact that Obi-wan and Yoda are still alive by the OT doesn't mean the Empire stopped looking for them.
"Kenobi resumed his pacing. "Vader used the training I gave him and the force within him for evil, to help the later corrupt Emperors. With the Jedi knights disbanded, disorganized, or dead, there were few to oppose Vader. Today they are all but extinct." - ANH novelization
Now, this isn't to say I don't understand your point, I just don't think the original scenario is so bad.