If it was a matter of programming, hesitation doesn't even come into it.
Weyland has words with him over it. Weyland shouldn't stand for that kind of behavior for even a second, because that is not how that character had been depicted up to that point. He's one of the biggest control freaks ever.
That’s not the way I see the Weyland character.
Yes, he likes to be in control (and overall he is in control) but he tolerates opposition from his associates, especially in a parent / child relationship.
* For instance Weyland’s comments to Vickers. From “Prometheus”;
Peter Weyland: After all your vigorous attempts to stop me from coming here, I’m surprised to see you...
Peter Weyland: Very negative way of looking at things.
- For Weyland, David is like a son.
There’s a man sitting with you today, his name is David. He is the closest thing to a son I will ever had,
* Weyland doesn’t want a mindless slave as a “son”.
He wants a clever, creative android who will be useful.
Such as with finding the living Engineer on LV-223.
* Weyland was never in any direct danger from David.
Even when David hints that he might want Weyland to be dead, he admits that with Weyland’s programming, he is not free to do what he wants.
Elizabeth Shaw: What happens when Weyland’s not around to program you anymore?
David: I suppose I’d be free...
David: ‘Want’; not a concept I’m familiar with. That being said, doesn’t everyone want their parents dead?
I'm saying it would have been far more interesting to me had they gone with something more philosophical between the two...
With all the androids in film or the betrayer characters in science fiction movies, I can’t find one that is more interesting than David, maybe just as good but not better; (that includes Ash, Data, C3PO, the androids in Spielberg’s “AI”, with human betrayers, Cypher or with just a computer, HAL).
* The opening sequence in “Covenant” has a giant statue of the Biblical David.
- Weyland obviously has pretensions to be godlike.
- David chooses to play Wagner’s “Entry of the Gods into Valhalla”.
- David is making a statement about himself which is just as pretentious as his creator.
That’s an interesting conflict.
Who will be the master in the long run?
The wealthy, controlling human?
Or the clever android?
* In human terms David is a sociopath. But he plays the role of obedient helper very well,
biding his time for years until he has the opportunity to strike.
- Yet, David at the same time seems to have really cared for Shaw, even though he tortured and killed her.
It’s a deranged mind similar to Norman Bates in Psycho.
Interesting stuff imo.