Summary Execution is an external factor - a Commissar can potentially leave the squad (if a Commissar Lord), but a standard bearer cannot!
Think of it in logical steps, and it becomes clear.
STEP 1: Determine if the unit must take a Morale Check.
STEP 2: Determine Leadership value.
Here is where the Standard kicks in - as far as the rules are concerned, a unit with re-rollable leadership has not failed its Morale Check unless the original roll and the re-roll have failed. Thus, the Standard is part of Step 2.
STEP 3: Special fall-back conditions.
This is where the Commissar comes in. Normally, a unit must fall back upon failing its Morale Check. However, a Commissar intervenes - Summary Execution applies here.
STEP 4: Fall-back movement.
As I have said, Summary Execution is not a re-roll. It is a re-take. For the Standard, there is no action between failing the initial roll and taking the re-roll. With Summary Execution, there is. Therefore, the Standard takes precedent due to lack of a "mid-step".