Why wasn't Dr. Erskine shot before he turned Steve into a super soldier?

The infiltrator did not have the access to kill Erskine until such time as the serum was ready to be demonstrated.

It's clear that the infiltrator (Heinz Kruger) as Fred Clemson had not visited the project before since he is introduced to Col. Philips who does not know him.

Then we also know that acquisition of the serum (and perhaps also denying it to the Allies) is the intention from the script.

               JOHANN SCHMIDT
 His serum is the Allies’ only
 defense against the power we now
 possess. If we take it away, our
 victory is assured.

So, as soon as the infiltrator sees that the serum succeeds he not only steals the last vial AND kills Erskine to deny it to apparently limit future development.

  THE MAN WITH GLASSES ENTERS THE LAB. Across the room, he
  spies...THE REMAINING TUBE OF UNUSED SERUM. He flicks open a
  lighter, revealing A BUTTON. 

  Kruger pushes the button.

 THE CIGARETTE CASE MAKES AN OMINOUS...CLICK.

   The booth EXPLODES, shooting FIRE AND GLASS into the lab.
    Phillips shoves Brandt out of the way. Peggy pulls a pistol.
    ERSKINE sees KRUGER making for the SERUM. He bolts to get to
   it first.

 KRUGER draws a PISTOL and SHOOTS the old man down.

Arguably, Kruger could just have killed Erksine as soon as he saw him but also obtaining the serum would have been an incredible bonus.

Because Zola doubted that Dr. Erskin will succeed.

Here is the conversation between Schmidt and Dr. Zola:

Zola: I just don't see why you need concern yourself.

Zola: I can't imagine he will succeed. Again.

In case he succeeds in making a serum, they also need to get the serum to snatch the only defense of allies in order to ensure their victory.

That conversation goes as follows:

Red Skull: His serum is the Allies' only defense against this power we now possess. If we take it away from them, then our victory is assured.

So, when the infiltrator saw Dr. Erskine experiment successful, he took the serum and shot him to ensure that they cannot work again on this experiment.

Technically, they did stop the super-soldier program. The original plan was to develop a squad/platoon/battalion of enhanced soldiers. Steve Rogers was a prototype, an example of what the program could accomplish. "If we can turn this puny specimen into a powerhouse, imagine what we can do with soldiers who are already well-trained and fit!"

Now, the Nazis know that this is possible. And the program is limited to one man.

After all, what can one man do...?